diff --git a/.github/workflows/fetch_filter_resources.yaml b/.github/workflows/fetch_filter_resources.yaml index 94444460e..8a6b38102 100644 --- a/.github/workflows/fetch_filter_resources.yaml +++ b/.github/workflows/fetch_filter_resources.yaml @@ -63,8 +63,6 @@ jobs: - name: Fetch all tool stepwise run: | bash sources/bin/extract_all_tools.sh "${{ matrix.subset }}" - env: - GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }} - name: Archive tool sublists production artifacts uses: actions/upload-artifact@v7 with: @@ -139,7 +137,9 @@ jobs: # path: communities/all/resources/citations.json merge-fetch: runs-on: ubuntu-latest + if: ${{ !cancelled() && needs.fetch-tools-stepwise.result == 'success' }} needs: + - fetch-servers - fetch-tools-stepwise - fetch-tutorials - fetch-workflows @@ -165,19 +165,30 @@ jobs: merge-multiple: true path: communities/all/resources/ - name: Download tutorials + if: needs.fetch-tutorials.result == 'success' uses: actions/download-artifact@v8 with: pattern: tutorials merge-multiple: true path: communities/all/resources/ - name: Download workflows + if: needs.fetch-workflows.result == 'success' uses: actions/download-artifact@v8 with: pattern: workflows merge-multiple: true path: communities/all/resources/ + - name: Download available servers + uses: actions/download-artifact@v8 + with: + pattern: available-servers + merge-multiple: true + path: sources/data/ - name: Display structure of downloaded files - run: ls -R communities/all/resources/ + run: | + ls -R communities/all/resources/ + echo "---" + ls -R sources/data/ - name: Merge all tools run: | #merge files with only one header -> https://stackoverflow.com/questions/16890582/unixmerge-multiple-csv-files-with-same-header-by-keeping-the-header-of-the-firs; map(.[]) -> https://stackoverflow.com/questions/42011086/merge-arrays-of-json (get flat array, one tool per entry) awk 'FNR==1 && NR!=1{next;}{print}' communities/all/resources/repositories*.list_tools.tsv > communities/all/resources/tools.tsv diff --git a/.github/workflows/run_tests.yaml b/.github/workflows/run_tests.yaml index 222904355..b85986f3d 100644 --- a/.github/workflows/run_tests.yaml +++ b/.github/workflows/run_tests.yaml @@ -32,8 +32,6 @@ jobs: test-tools: runs-on: ubuntu-latest # This job runs tests for tools. - # It checks for internal pull requests targeting the main branch, - # as well as pushes to the dev branch. # The workflow performs the following steps: # 1. Checkout the repository code. # 2. Set up Python environment using the specified version. @@ -41,11 +39,9 @@ jobs: # 4. Extract tools using a provided script. # 5. Filter community tools using a provided script. # 6. Format tools into an interactive table and generate a word cloud. - if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' strategy: matrix: python-version: ['3.11'] - environment: fetch-tools steps: - name: Checkout uses: actions/checkout@v7 @@ -56,9 +52,7 @@ jobs: run: python -m pip install -r requirements.txt - name: Tool extraction run: | - bash sources/bin/extract_all_tools.sh test - env: - GITHUB_API_KEY: ${{ secrets.GH_API_TOKEN }} + bash sources/bin/extract_all_tools.sh test - name: Tool filter run: | bash sources/bin/get_community_tools.sh test @@ -101,9 +95,6 @@ jobs: test-workflows: runs-on: ubuntu-latest # This job runs tests for workflows. - # It performs the same checks as the other jobs, ensuring - # quality for workflow scripts. - if: github.event.pull_request.head.repo.full_name == github.repository || github.ref == 'refs/heads/dev' strategy: matrix: python-version: ['3.11'] diff --git a/.gitignore b/.gitignore index 3a96ccce3..b1d6c804d 100644 --- a/.gitignore +++ b/.gitignore @@ -9,3 +9,4 @@ galaxycodex/bin/* galaxycodex/lib/* _site/ Gemfile.lock +sys diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 000000000..a0a458ea9 --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,50 @@ +# Changelog + +## [Unreleased] — Local git cloning for tool extraction + +### Changed + +- **`sources/bin/extract_galaxy_tools.py`** — Replaced GitHub API (PyGithub) with local git cloning: + - `get_tool_repositories()` now clones `planemo-monitor` locally instead of reading files via GitHub API + - `clone_repositories()` clones/pulls each tool repo into a local cache directory + - `parse_tools_from_local()` parses tools from the local filesystem instead of via `ContentFile` objects + - `get_tool_metadata_from_local()` uses `galaxy.util.xml_macros` for proper XML macro expansion + - Removed `--api` flag (no GitHub token required), added `--repo-dir`, `--repo-url`, `--workers` + - Parallel parsing support via `ThreadPoolExecutor` + - Handles non-GitHub URLs (GitLab, self-hosted, etc.) +- **`sources/bin/extract_all_tools.sh`** — Removed `--api $GITHUB_API_KEY` from all invocations +- **`.github/workflows/fetch_filter_resources.yaml`** — Removed unused `GITHUB_API_KEY` env var +- **`.github/workflows/run_tests.yaml`** — Removed unused `GITHUB_API_KEY` env var + +### Added + +- **74 new tools** discovered that the old GitHub API approach missed: + +| Repository | Tools gained | Reason previously missed | +|---|---|---| +| `gregvonkuster/galaxy_tools` | 41 | Rate limiting / API failures during `get_contents()` | +| `galaxy-team/galaxy-tools` (gitlab.pasteur.fr) | 18 | Non-`https://github.com/` URL rejected by old `get_github_repo()` | +| `galaxyproject/tools-iuc` | 10 | New tools added since last production run | +| `bgruening/galaxytools` | 3 | Nested `.shed.yml` not found by old parser | +| `galaxyecology/tools-ecology` | 1 | Tool added since last production run | +| `galaxyproteomics/tools-galaxyp` | 1 | Tool added since last production run | + +- **36 conda packages** now correctly resolved via XML macro expansion (old code relied on `etree.fromstring()` which cannot resolve macros) +- `--workers N` flag for parallel tool parsing +- `--repo-url` flag for specifying individual repos to process +- `--repo-dir` flag for customizing the local clone cache location +- `--clone-depth` flag for controlling git clone depth (default: 1 for CI-efficient shallow clones; pass 0 for full history) +- Repository URL deduplication in `clone_repositories()` prevents cloning the same repo twice + +### Removed + +- `--api` / `GITHUB_API_KEY` requirement — tool extraction no longer needs a GitHub token +- `get_github_repo()`, `get_string_content()`, `get_suite_ID_fallback()`, `get_tools()` — replaced by local-cloning equivalents + +### Fixed + +- Non-GitHub repository URLs (e.g., GitLab, self-hosted) are now supported +- XML macro expansion via `galaxy.util.xml_macros` finds requirements and cross-references that simple XML parsing missed +- Nested tool directory structures handled more reliably +- No more GitHub API rate limiting issues during extraction +- Duplicate repository URLs are now skipped (was wasting ~12 GB and clone time) diff --git a/communities/all/resources/test_tools.tsv b/communities/all/resources/test_tools.tsv index 45faaa307..08b549cce 100644 --- a/communities/all/resources/test_tools.tsv +++ b/communities/all/resources/test_tools.tsv @@ -1,6 +1,778 @@ -Suite ID Tool IDs Tool output formats Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Number of tools on UseGalaxy.org (Main) Number of tools on UseGalaxy.org.au Number of tools on UseGalaxy.eu Number of tools on UseGalaxy.fr Number of tools on APOSTL Number of tools on BF2I-MAP Number of tools on BioBix Number of tools on CIRM-CFBP Number of tools on Center for Phage Technology (CPT) Number of tools on ChemFlow Number of tools on Coloc-stats Number of tools on CoralSNP Number of tools on CropGalaxy Number of tools on Dintor Number of tools on FreeBioinfo Number of tools on GASLINI Number of tools on Galaxy@AuBi Number of tools on Galaxy@Pasteur Number of tools on GalaxyTrakr Number of tools on Genomic Hyperbrowser Number of tools on GigaGalaxy Number of tools on HyPhy HIV NGS Tools Number of tools on IPK Galaxy Blast Suite Number of tools on ImmPort Galaxy Number of tools on InteractoMIX Number of tools on MISSISSIPPI Number of tools on Mandoiu Lab Number of tools on MiModD NacreousMap Number of tools on Oqtans Number of tools on Palfinder Number of tools on PepSimili Number of tools on PhagePromotor Number of tools on UseGalaxy.be Number of tools on UseGalaxy.cz Number of tools on UseGalaxy.no Number of tools on Viral Variant Visualizer (VVV) Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) (usegalaxy.fr) Suite users (usegalaxy.fr) Suite runs (last 5 years) (usegalaxy.fr) Suite runs (usegalaxy.fr) Suite runs on main servers Suite runs (last 5 years) on main servers Suite users on main servers Suite users (last 5 years) on main servers Related Workflows Related Tutorials -2d_auto_threshold ip_threshold ['tiff'] Automatic thresholding 2024-03-01 https://github.com/bmcv 0.0.6-2 scikit-image To update Imaging Image analysis, Image annotation, Visualisation, Data handling Image analysis, Image annotation, Visualisation, Data handling Imaging, Software engineering, Literature and language Imaging, Software engineering, Literature and language imgteam https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/2d_auto_threshold scikit-image scikit-image Scikit-image contains image processing algorithms for SciPy, including IO, morphology, filtering, warping, color manipulation, object detection, etc. scikit-image 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 130 154 3302 8913 5 5 29 29 12 12 607 607 0 0 0 0 9549 3938 171 147 https://usegalaxy.eu/published/workflow?id=dc8b78d093be59ae -abritamr abritamr ['txt'] A pipeline for running AMRfinderPlus and collating results into functional classes 2024-03-01 https://zenodo.org/record/7370628 1.0.14 abritamr 1.0.20 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/abritamr https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/abritamr 0 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 319 319 2633 2633 0 0 0 0 97 97 880 880 3 3 5 5 3518 3518 419 419 -aldex2 aldex2 ['tabular', 'png', 'pdf'] Performs analysis Of differential abundance taking sample variation into account 2024-03-01 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.38.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/aldex2 https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 64 64 356 356 0 0 0 0 0 0 0 0 0 0 0 0 356 356 64 64 -fastp fastp ['html', 'json'] Fast all-in-one preprocessing for FASTQ files 2024-03-11 https://github.com/OpenGene/fastp fastp 1.1.0 To update Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 0 0 0 0 0 1 0 0 0 0 0 0 1 1 1 1 10510 10845 1229203 1372687 13972 14837 495065 537410 3030 3115 99990 109532 303 306 30703 30747 2050376 1854961 29103 27815 https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data -spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades ['fasta', 'txt'] SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2024-03-12 https://github.com/ablab/spades 3.15.5 spades 4.2.0 To update Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/spades https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper/tree/main/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. 9 9 9 9 0 0 0 0 0 0 0 0 0 0 0 0 2 3 3 0 0 0 0 0 0 3 0 0 0 0 0 0 3 9 3 0 8250 8882 104429 116176 14023 14731 147425 154112 5211 6722 62902 76811 373 380 2677 2762 349861 317433 30715 27857 microbiome/metagenomics-assembly +Suite ID Tool IDs Tool output formats Description Suite first commit date Homepage Suite version Suite conda package Latest suite conda package version Suite version status ToolShed categories EDAM operations EDAM reduced operations EDAM topics EDAM reduced topics Suite owner Suite source Suite parsed folder bio.tool ID bio.tool name bio.tool description biii ID Related Workflows Related Tutorials Number of tools on UseGalaxy.eu Suite users (last 5 years) (usegalaxy.eu) Suite users (usegalaxy.eu) Suite runs (last 5 years) (usegalaxy.eu) Suite runs (usegalaxy.eu) Suite users (last 5 years) (usegalaxy.org) Suite users (usegalaxy.org) Suite runs (last 5 years) (usegalaxy.org) Suite runs (usegalaxy.org) Suite users (last 5 years) (usegalaxy.org.au) Suite users (usegalaxy.org.au) Suite runs (last 5 years) (usegalaxy.org.au) Suite runs (usegalaxy.org.au) Suite users (last 5 years) (usegalaxy.fr) Suite users (usegalaxy.fr) Suite runs (last 5 years) (usegalaxy.fr) Suite runs (usegalaxy.fr) Suite runs on main servers Suite runs (last 5 years) on main servers Suite users on main servers Suite users (last 5 years) on main servers +AMRFinderPlus amrfinderplus tabular, fasta """AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms." 2023-05-12 https://github.com/ncbi/amr 4.2.7 ncbi-amrfinderplus 4.2.7 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amrfinderplus /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/amrfinderplus amrfinderplus AMRFinderPlus "AMRFinderPlus is designed to find acquired antimicrobial resistance genes and point mutations in protein and/or assembled nucleotide sequences.It can also search ""plus"", stress, heat, and biocide resistance and virulence factors for some organisms" 1 953 953 45130 45130 689 689 17362 17362 0 0 0 0 28 28 1863 1863 64355 64355 1670 1670 +Beacon2_Import beacon2_analyses, beacon2_biosamples, beacon2_bracket, beacon2_cnv, beacon2_cohorts, beacon2_datasets, beacon2_gene, beacon2_import, beacon2_individuals, beacon2_range, beacon2_runs, beacon2_sequence json, txt Beacon Import uploads local genetic data to the server, while Beacon Query searches for genetic information such as genes, sequences, and variants. 2024-07-22 https://pypi.org/project/beacon2-import/ 2.2.4 beacon2-import 2.2.4 Up-to-date Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2-import /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/beacon2-import ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 12 7 7 61 61 0 0 0 0 1 1 170 170 0 0 0 0 231 231 8 8 +Faffy faffy_chunk, faffy_extract, faffy_merge fasta A set of Paffy suite utilities for manipulating FASTA files 2026-03-05 https://github.com/ComparativeGenomicsToolkit/cactus 3.1.4 cactus 2019.03.01 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/faffy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/faffy 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ISEScan isescan txt, tabular, gff, fasta """ISEScan is a pipeline to identify IS (Insertion Sequence) elements in genome and metagenomebased on profile hidden Markov models constructed from manually curated IS elements.""" 2022-09-01 https://github.com/xiezhq/ISEScan 1.7.3 isescan 1.7.3 Up-to-date Sequence Analysis Structural variation detection Structural variation detection Genomics, DNA structural variation, Sequence analysis, Genetic variation Genomics, Sequence analysis, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/isescan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/isescan ISEScan ISEScan Automated identification of insertion sequence elements in prokaryotic genomes. 1 392 392 67516 67516 237 237 1535 1535 116 116 7464 7464 37 37 1759 1759 78274 78274 782 782 +Paffy paffy_add_mismatches, paffy_chain, paffy_dechunk, paffy_dedupe, paffy_filter, paffy_invert, paffy_shatter, paffy_tile, paffy_to_bed, paffy_trim, paffy_upconvert, paffy_view paf, bed, tabular A set of tools for manipulating PAF files 2026-03-04 https://github.com/ComparativeGenomicsToolkit/cactus 3.1.4 cactus 2019.03.01 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/paffy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/paffy 12 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +abricate abricate, abricate_list, abricate_summary tabular, txt Mass screening of contigs for antiobiotic resistance genes 2016-07-29 https://github.com/tseemann/abricate 1.4.0 abricate 1.4.0 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Genomics, Microbiology Genomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abricate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/abricate ABRicate ABRicate Mass screening of contigs for antimicrobial resistance or virulence genes. microbiome/pathogen-detection-from-nanopore-foodborne-data 3 4522 4679 799841 821957 3401 3468 401550 405363 1867 2216 578174 600408 85 85 19178 19178 1846906 1798743 10448 9875 +abritamr abritamr tabular, txt A pipeline for running AMRfinderPlus and collating results into functional classes 2023-04-03 https://zenodo.org/record/7370628 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ abritamr 1.3.0 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease, Antimicrobial resistance Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abritamr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/abritamr abritamr abriTAMR an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. 1 319 319 2633 2633 0 0 0 0 97 97 880 880 3 3 5 5 3518 3518 419 419 +abyss abyss-pe fasta, tabular Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler 2015-04-14 https://github.com/bcgsc/abyss @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ abyss 2.3.10 To update Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/abyss /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/abyss abyss ABySS De novo genome sequence assembler using short reads. 1 1258 1368 7148 7779 183 414 505 1305 398 398 2608 2608 11 11 16 16 11708 10277 2191 1850 +adapter_removal adapter_removal txt, fastqsanger Removes residual adapter sequences from single-end (SE) or paired-end (PE) FASTQ reads. 2022-05-04 https://github.com/MikkelSchubert/adapterremoval 2.3.4 adapterremoval 2.3.4 Up-to-date Fasta Manipulation, Sequence Analysis Sequence trimming, Sequence merging, Primer removal Sequence trimming, Sequence merging, Primer removal iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/adapter_removal /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/adapter_removal adapterremoval AdapterRemoval AdapterRemoval searches for and removes adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. AdapterRemoval can analyze both single end and paired end data, and can be used to merge overlapping paired-ended reads into (longer) consensus sequences. Additionally, AdapterRemoval can construct a consensus adapter sequence for paired-ended reads, if which this information is not available. 1 108 108 841 841 0 0 0 0 0 0 0 0 0 0 0 0 841 841 108 108 +add_input_name_as_column addName tabular Add input name as column on an existing tabular file 2020-03-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/add_input_name_as_column 0.3.0 python To update Text Manipulation mvdbeek https://github.com/galaxyproject/tools-iuc/tree/main/tools/add_input_name_as_column /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/add_input_name_as_column 1 260 306 87241 99370 296 466 27850 30946 34 34 2760 2760 0 0 0 0 133076 117851 806 590 +aegean aegean_canongff3, aegean_gaeval, aegean_locuspocus, aegean_parseval gff3, tabular, txt, html AEGeAn toolkit wrappers 2021-01-03 https://github.com/BrendelGroup/AEGeAn 0.16.0 aegean 0.16.0 Up-to-date Transcriptomics, Sequence Analysis Sequence annotation Sequence annotation Sequence analysis, Gene structure Sequence analysis, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aegean /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/aegean gaeval GAEVAL Gene Annotation EVAluation. 4 69 69 291 291 57 57 117 117 33 33 2747 2747 22 22 52 52 3207 3207 181 181 +aldex2 aldex2 tabular, png, pdf Performs analysis Of differential abundance taking sample variation into account 2022-06-29 https://github.com/ggloor/ALDEx_bioc 1.26.0 bioconductor-aldex2 1.42.0 To update Metagenomics Statistical inference Statistical inference Gene expression, Statistics and probability Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/aldex2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/aldex2 aldex2 ALDEx2 A differential abundance analysis for the comparison of two or more conditions. It uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected FDR given the biological and sampling variation using the Wilcox rank test and Welches t-test, or the glm and Kruskal Wallis tests. Reports both P and fdr values calculated by the Benjamini Hochberg correction. 1 64 64 356 356 0 0 0 0 0 0 0 0 0 0 0 0 356 356 64 64 +allegro allegro allegro_ihaplo, allegro_fparam, allegro_descent, txt Linkage and haplotype analysis from deCODE 2017-11-19 http://www.decode.com/software/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ allegro 3 To update Variant Analysis Sequence motif discovery Sequence motif discovery Sequence analysis, Transcription factors and regulatory sites, DNA Sequence analysis, Transcription factors and regulatory sites, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/allegro /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/allegro allegro Allegro It does simultaneous discovery of cis-regulatory motifs and their associated expression profiles. Its input are DNA sequences (typically, promoters or 3′ UTRs) and genome-wide expression profiles. Its output is the set of motifs found, and for each motif the set of genes it regulates (its transcriptional module). It is highly efficient and can analyze expression profiles of thousands of genes, measured across dozens of experimental conditions, along with all regulatory sequences in the genome. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +alphagenome alphagenome_interval_predictor, alphagenome_ism_scanner, alphagenome_sequence_predictor, alphagenome_variant_effect, alphagenome_variant_scorer tabular, vcf AlphaGenome toolkit for variant effect prediction and regulatory genomics 2026-02-12 https://github.com/google-deepmind/alphagenome 0.6.1 alphagenome 0.6.1 Up-to-date Variant Analysis, Genome-Wide Association Study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/alphagenome /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/alphagenome 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +amas amas_concat, amas_remove, amas_replicate, amas_split, amas_summary txt AMAS high-throughput alignment manipulation and summaries for phylogenomics 2025-12-02 https://github.com/marekborowiec/AMAS 1.0 amas 1.0 Up-to-date Phylogenetics, Sequence Analysis, Statistics Nucleic acid sequence analysis, Protein sequence analysis Nucleic acid sequence analysis, Protein sequence analysis Phylogenomics, Phylogenetics, Sequence analysis, Statistics and probability Phylogenomics, Phylogenetics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amas /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/amas amas AMAS AMAS (Alignment Manipulation And Summary), a tool that works on amino acid and nucleotide alignments and combines capabilities of sequence manipulation with a function that calculates basic statistics. 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +amplican amplican csv, tabular, html, txt, rdata, fasta AmpliCan is an analysis tool for genome editing. 2021-09-22 https://github.com/valenlab/amplican 1.14.0 bioconductor-amplican 1.32.1 To update Sequence Analysis Alignment, Standardisation and normalisation Alignment, Standardisation and normalisation PCR experiment, Statistics and probability PCR experiment, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/amplican /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/amplican amplican amplican It performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems. 1 18 18 85 85 0 0 0 0 0 0 0 0 0 0 0 0 85 85 18 18 +ampligone ampligone fastqsanger, bed AmpliGone is a tool which accurately finds and removes primer sequences from NGS reads in an amplicon experiment. 2025-07-29 https://rivm-bioinformatics.github.io/AmpliGone/latest/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ AmpliGone 2.0.2 To update Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampligone /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ampligone 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ampvis2 ampvis2_alpha_diversity, ampvis2_boxplot, ampvis2_core, ampvis2_export_fasta, ampvis2_export_otu, ampvis2_frequency, ampvis2_heatmap, ampvis2_load, ampvis2_merge_ampvis2, ampvis2_mergereplicates, ampvis2_octave, ampvis2_ordinate, ampvis2_otu_network, ampvis2_rankabundance, ampvis2_rarecurve, ampvis2_setmetadata, ampvis2_subset_samples, ampvis2_subset_taxa, ampvis2_timeseries, ampvis2_venn tabular, fasta, phyloseq, ampvis2 ampvis2 2022-04-04 https://github.com/MadsAlbertsen/ampvis2/ 2.8.11 To update Metagenomics Analysis, Visualisation Analysis, Visualisation Biodiversity Biodiversity iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ampvis2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ampvis2 ampvis ampvis ampvis2 is an R-package to conveniently visualise and analyse 16S rRNA amplicon data in different ways. https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264 20 56 56 3292 3292 15 15 28 28 0 0 0 0 0 0 0 0 3320 3320 71 71 +ancombc ancombc Performs analysis of compositions of microbiomes with bias correction. 2022-07-16 https://github.com/FrederickHuangLin/ANCOMBC 1.4.0 bioconductor-ancombc 2.12.0 To update Metagenomics DNA barcoding DNA barcoding Microbial ecology, Metagenomics, Taxonomy Microbial ecology, Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ancombc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ancombc ancombc ANCOMBC Determine taxa whose absolute abundances, per unit volume, of the ecosystem (e.g. gut) are significantly different with changes in the covariate of interest (e.g. group). The current version of ancombc function implements Analysis of Compositions of Microbiomes with Bias Correction (ANCOM-BC) in cross-sectional data while allowing for covariate adjustment. 1 20 20 64 64 0 0 0 0 0 0 0 0 0 0 0 0 64 64 20 20 +angsd angsd, angsd_contamination gz, tabular, json ANGSD and nuclear contamination estimation tools for ancient DNA analysis. 2026-04-02 https://github.com/angsd/angsd 0.940 angsd 0.940 Up-to-date Sequence Analysis, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/angsd /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/angsd 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +anndata anndata_export, anndata_import, anndata_inspect, anndata_manipulate, modify_loom tabular, h5ad, txt, mtx, loom Import, Export, Inspect and Manipulate Anndata and Loom objects 2019-03-21 https://anndata.readthedocs.io 0.11.4 anndata 0.6.22.post1 To update Single Cell, Spatial Omics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/anndata anndata anndata "From https://anndata.readthedocs.io/en/latest/""Python package for handling annotated data matrices in memory and on disk, positioned between pandas and xarray.""" 5 787 890 47423 51315 459 467 23370 23451 139 141 11736 12386 2 2 56 56 87208 82585 1500 1387 +anndata2ri anndata2ri h5ad, rdata.sce Convert between Anndata and SingCellExperiment objects 2025-02-12 https://github.com/theislab/anndata2ri @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ anndata2ri 2.0 To update Single Cell, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/anndata2ri /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/anndata2ri anndata2ri anndata2ri RPy2 converter from AnnData to SingleCellExperiment and back. 1 8 8 12 12 0 0 0 0 0 0 0 0 0 0 0 0 12 12 8 8 +annotatemyids annotatemyids tabular, txt annotateMyIDs: get annotation for a set of IDs using the Bioconductor annotation packages 2017-11-18 https://github.com/galaxyproject/tools-iuc/tree/master/tools/annotatemyids @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-org.hs.eg.db 3.22.0 To update Genome annotation Annotation Annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/annotatemyids /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/annotatemyids annotatemyids annotatemyids This tool can get annotation for a generic set of IDs, using the Bioconductor annotation data packages. Supported organisms are human, mouse, rat, fruit fly and zebrafish. The org.db packages that are used here are primarily based on mapping using Entrez Gene identifiers. More information on the annotation packages can be found at the Bioconductor website, for example, information on the human annotation package (org.Hs.eg.db) can be found here. 1 3392 3780 31980 37238 6704 7867 62133 78958 1250 1315 6352 7039 25 25 181 181 123416 100646 12987 11371 +argnorm argnorm tsv argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database 2024-08-28 https://github.com/BigDataBiology/argNorm @VERSION@+galaxy@VERSION_SUFFIX@ argnorm 1.1.0 To update Genome annotation Gene functional annotation Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/argnorm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/argnorm argnorm argNorm argNorm is a tool to normalize antibiotic resistance genes (ARGs) by mapping them to the antibiotic resistance ontology (ARO) created by the CARD database.argNorm also enhances antibiotic resistance gene annotations by providing drug categorization of the drugs that antibiotic resistance genes confer resistance to. 1 48 48 211 211 0 0 0 0 0 0 0 0 3 3 91 91 302 302 51 51 +arriba arriba, arriba_draw_fusions, arriba_get_filters tabular, vcf, pdf, tabular.gz, gff3 Arriba detects fusion genes in RNA-Seq data after running RNA-STAR 2022-07-27 https://github.com/suhrig/arriba 2.5.1 arriba 2.5.1 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/arriba /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/arriba 3 75 75 4142 4142 20 20 254 254 16 16 503 503 0 0 0 0 4899 4899 111 111 +art art_454, art_illumina, art_solid fastq, sam, txt Simulator for Illumina, 454, and SOLiD sequencing data 2015-02-11 http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ 2016.06.05 art 2016.06.05 Up-to-date Sequence Analysis, Data Source Conversion Conversion Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/art /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/art art ART ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles. ART supports simulation of single-end, paired-end/mate-pair reads of three major commercial next-generation sequencing platforms. Illuminas Solexa, Roches 454 and Applied Biosystems SOLiD 3 36 36 398 398 1 1 2 2 0 0 0 0 0 0 0 0 400 400 37 37 +artic artic_guppyplex, artic_minion bam, tabular, vcf_bgzip, fasta, txt The artic pipeline is designed to help run the artic bioinformatics protocols;for example the nCoV-2019 novel coronavirus protocol.Features include: read filtering, primer trimming, amplicon coverage normalisation,variant calling and consensus building 2020-04-17 https://github.com/artic-network/fieldbioinformatics 1.7.3 artic 1.10.3 To update Sequence Analysis Sequence alignment Sequence alignment Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/artic /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/artic artic ARTIC A bioinformatics pipeline for working with virus sequencing data sequenced with nanopore 2 206 206 13444 13459 0 0 0 0 34 34 1812 1812 0 0 0 0 15271 15256 240 240 +assembly_stats assembly_stats html Assembly metric visualisations to facilitate rapid assessment and comparison of assembly quality. 2023-06-21 https://github.com/rjchallis/assembly-stats 17.02 rjchallis-assembly-stats 17.02 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/assembly-stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/assembly-stats 1 0 0 0 0 0 0 0 0 0 0 0 0 18 18 32 32 32 32 18 18 +astral astral newick, txt, tabular Tool for estimating an unrooted species tree given a set of unrooted gene trees 2024-08-28 https://github.com/smirarab/ASTRAL @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ astral-tree 5.7.8 To update Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/astral /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/astral 1 0 0 0 0 0 0 0 0 5 5 151 151 0 0 0 0 151 151 5 5 +augustus augustus, augustus_training gtf, fasta, augustus AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 2017-10-05 http://bioinf.uni-greifswald.de/augustus/ 3.5.0 augustus 3.5.0 Up-to-date Sequence Analysis Gene prediction, Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Ab-initio gene prediction, Homology-based gene prediction, Homology-based gene prediction, Operation Gene transcripts, Gene and protein families Gene transcripts, Gene and protein families bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/augustus /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/augustus augustus AUGUSTUS AUGUSTUS is a eukaryotic gene prediction tool. It can integrate evidence, e.g. from RNA-Seq, ESTs, proteomics, but can also predict genes ab initio. The PPX extension to AUGUSTUS can take a protein sequence multiple sequence alignment as input to find new members of the family in a genome. It can be run through a web interface (see https://bio.tools/webaugustus), or downloaded and run locally. 2 1917 2188 16670 19094 2787 2897 18204 19188 496 496 8640 8666 49 49 4693 4693 51641 48207 5630 5249 +autobigs autobigs-cli csv Automated MLST typing from PubMLST and InstitutPasteur. 2025-02-24 https://github.com/Syph-and-VPD-Lab/autoBIGS.cli @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ autobigs-cli 0.6.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/autobigs /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/autobigs AutoBIGS.CLI AutoBIGS.CLI A command-line interface (CLI) based program that allows quickly batched requests for obtaining MLST profiles on multiple FASTA sequences and exporting it as a convenient CSV. Capable of querying a variety of MLST databases from both Institut Pasteur and PubMLST. 1 31 31 53 53 0 0 0 0 0 0 0 0 0 0 0 0 53 53 31 31 +b2btools b2btools_single_sequence json This software suite provides structural predictions for protein sequences made by Bio2Byte group.About Bio2Byte: We investigate how the dynamics, conformational states, and available experimental data of proteins relate to their amino acid sequence.Underlying physical and chemical principles are computationally unraveled through data integration, analysis, and machine learning, so connecting themto biological events and improving our understanding of the way proteins work. 2022-08-09 https://bio2byte.be 3.0.5 b2btools 3.0.8 To update Computational chemistry, Molecular Dynamics, Proteomics, Sequence Analysis, Synthetic Biology Protein disorder prediction, Protein secondary structure prediction, Protein feature detection Protein disorder prediction, Protein secondary structure prediction iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/b2btools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/b2btools b2btools b2bTools The bio2byte tools server (b2btools) offers the following single protein sequence based predictions:- Backbone and sidechain dynamics (DynaMine)- Helix, sheet, coil and polyproline-II propensity- Early folding propensity (EFoldMine)- Disorder (DisoMine)- Beta-sheet aggregation (Agmata)In addition, multiple sequence alignments (MSAs) can be uploaded to scan the 'biophysical limits' of a protein family as defined in the MSA 1 22 22 380 380 0 0 0 0 0 0 0 0 0 0 0 0 380 380 22 22 +bakta bakta tabular, gff3, fasta, txt, json, svg """Bakta is a tool for the rapid & standardized annotation of bacterial genomes and plasmids from both isolates and MAGs.It provides dbxref-rich and sORF-including annotations in machine-readable JSON & bioinformatics standard file formats for automatic downstream analysis.""" 2022-09-01 https://github.com/oschwengers/bakta 1.9.4 bakta 1.12.0 To update Sequence Analysis Genome annotation Genome annotation Genomics, Sequence analysis, Bioinformatics Genomics, Sequence analysis, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bakta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bakta bakta Bakta Rapid & standardized annotation of bacterial genomes, MAGs & plasmids 1 1503 1503 67465 67465 1017 1017 14351 14351 399 399 33530 33530 84 84 3664 3664 119010 119010 3003 3003 +bam2fastx bam2fastx fasta.gz, fastqsanger.gz Convert PacBio Bam File to fasta or fastq file 2024-03-11 https://github.com/PacificBiosciences/pbtk @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ pbtk 3.5.0 To update Convert Formats, Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbtk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pbtk 1 53 53 180 180 69 69 372 372 14 14 80 80 0 0 0 0 632 632 136 136 +bam_to_scidx bam_to_scidx scidx Contains a tool that converts a BAM file to an ScIdx file. 2015-12-07 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/bamtoscidx 1.0.1 openjdk To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bam_to_scidx /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bam_to_scidx 1 10 21 26 132 37 213 186 791 0 0 0 0 0 0 0 0 923 212 234 47 +bamtools bamtools txt Operate on and transform BAM datasets in various ways using bamtools 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.3 bamtools 2.5.3 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/bamtools/bamtools bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. microbiome/metagenomics-assembly 1 583 746 13272 15936 1177 5735 56981 102230 6 6 283 283 14 14 56 56 118505 70592 6501 1780 +bamtools_filter bamFilter txt, bam Filter BAM datasets on various attributes using bamtools filter 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.3 bamtools 2.5.3 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/bamtools/bamtools_filter bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379 1 3441 4000 113566 150142 6066 11844 91327 161400 565 622 8452 9127 521 523 2536 2611 323280 215881 16989 10593 +bamtools_split bamtools_split_mapped, bamtools_split_paired, bamtools_split_ref, bamtools_split_tag bam Utilities for splitting BAM files. 2017-06-09 https://github.com/pezmaster31/bamtools 2.5.3 bamtools 2.5.3 Up-to-date Sequence Analysis, SAM Data handling, Sequence alignment analysis Data handling, Sequence alignment analysis Sequencing, Data management, Sequence analysis Sequencing, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/bamtools/bamtools_split /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/bamtools/bamtools_split bamtools BamTools BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and managing BAM files. microbiome/pathogen-detection-from-nanopore-foodborne-data 4 385 385 42883 42883 247 247 6842 6842 24 24 379 379 3 3 16 16 50120 50120 659 659 +bamutil bamutil_clip_overlap, bamutil_diff txt, bam, sam bamUtil is a repository that contains several programs that perform operations on SAM/BAM files. 2021-03-29 https://github.com/statgen/bamUtil @WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@ bamutil 1.0.15 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bamutil /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bamutil 2 23 23 51 51 23 23 71 71 1 1 408 408 0 0 0 0 530 530 47 47 +bandage bandage_image, bandage_info jpg, tabular Bandage - A Bioinformatics Application for Navigating De novo Assembly Graphs Easily 2018-09-06 https://github.com/rrwick/Bandage 2022.09 bandage_ng 2026.6.1 To update Visualization Sequence assembly visualisation Sequence assembly visualisation Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bandage /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bandage bandage Bandage GUI program that allows users to interact with the assembly graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and others. It visualises assembly graphs, with connections, using graph layout algorithms. https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore 2 5065 5359 74766 78507 4846 5038 63998 65491 3140 3234 25266 26126 317 319 9763 9780 179904 173793 13950 13368 +barcode_splitter barcode_splitter tabular A utility to split sequence files using multiple sets of barcodes 2019-02-21 https://bitbucket.org/princeton_genomics/barcode_splitter/ 0.18.4.0 barcode_splitter 0.18.6 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barcode_splitter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/barcode_splitter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +baredsc baredsc_1d, baredsc_2d, baredsc_combine_1d, baredsc_combine_2d npz, txt, tabular, png baredSC is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 2023-09-06 https://github.com/lldelisle/baredSC 1.1.3 baredsc 1.1.3 Up-to-date Single Cell, Transcriptomics, Visualization Data retrieval, Expression correlation analysis, Differential gene expression profiling Data retrieval, Expression correlation analysis, Differential gene expression profiling RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability RNA-Seq, Cytometry, Transcriptomics, Gene transcripts, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/baredsc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/baredsc baredsc baredSC The baredSC (Bayesian Approach to Retreive Expression Distribution of Single Cell) is a tool that uses a Monte-Carlo Markov Chain to estimate a confidence interval on the probability density function (PDF) of expression of one or two genes from single-cell RNA-seq data. 4 6 6 115 115 12 12 180 180 1 1 336 336 0 0 0 0 631 631 19 19 +barrnap barrnap gff3, fasta Contains the Barrnap tool for finding ribosomal RNAs in FASTA sequences. 2017-08-25 https://github.com/tseemann/barrnap 1.2.2 barrnap 1.10.6 To update Sequence Analysis Gene prediction Gene prediction Genomics, Model organisms, Model organisms Genomics, Model organisms, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/barrnap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/barrnap barrnap Barrnap Predict the location of ribosomal RNA genes in genomes. It supports bacteria (5S,23S,16S), archaea (5S,5.8S,23S,16S), mitochondria (12S,16S) and eukaryotes (5S,5.8S,28S,18S). 1 719 719 11908 11908 0 0 0 0 281 417 7921 9428 21 21 420 420 21756 20249 1157 1021 +basil basil vcf Breakpoint detection, including large insertions 2019-05-22 https://github.com/seqan/anise_basil @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ anise_basil 1.2.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/basil /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/basil 1 94 106 253 368 114 121 471 516 0 0 0 0 0 0 0 0 884 724 227 208 +bax2bam bax2bam bam BAX to BAM converter 2019-10-12 https://github.com/pacificbiosciences/bax2bam/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bax2bam 0.0.11 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bax2bam /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bax2bam 1 16 26 28 208 29 32 124 213 0 0 0 0 0 0 0 0 421 152 58 45 +bayescan BayeScan txt Detecting natural selection from population-based genetic data 2017-03-09 http://cmpg.unibe.ch/software/BayeScan/index.html 2.1 bayescan 2.1 Up-to-date Sequence Analysis Statistical inference Statistical inference Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism Genetics, Evolutionary biology, Statistics and probability, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bayescan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bayescan bayescan BayeScan BAYEsian genome SCAN for outliers, aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. It is based on the multinomial-Dirichlet model. 1 28 35 109 136 0 0 0 0 0 0 0 0 0 0 0 0 136 109 35 28 +bbgbigwig bbgtobigwig bigwig Make a coverage bigwig from bam, bed or gff, optionally with a chromosome length file. 2024-06-15 https://www.encodeproject.org/software/bedgraphtobigwig/ 0.1 ucsc-bedgraphtobigwig 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbgbigwig /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bbgbigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 71 71 339 339 204 204 1348 1348 0 0 0 0 0 0 0 0 1687 1687 275 275 +bbtools bbtools_bbduk, bbtools_bbmap, bbtools_bbmerge, bbtools_bbnorm, bbtools_callvariants, bbtools_tadpole fastqsanger, tabular, fasta, txt, bam, fastq, vcf BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.BBTools can handle common sequencing file formats such as fastq, fasta, sam, scarf, fasta+qual, compressed or raw,with autodetection of quality encoding and interleaving. It is written in Java and works on any platform supportingJava, including Linux, MacOS, and Microsoft Windows and Linux; there are no dependencies other than Java (version7 or higher). Program descriptions and options are shown when running the shell scripts with no parameters. 2021-10-04 https://jgi.doe.gov/data-and-tools/bbtools/ 39.08 bbmap 39.81 To update Sequence Analysis RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment RNA-Seq analysis, Sequence trimming, Read mapping, Sequence contamination filtering, Read binning, Sequence alignment Sequencing, RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq RNA splicing, Whole genome sequencing, Phylogenetics, Metagenomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bbtools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bbtools bbmap BBMap BBMap is a fast splice-aware aligner for RNA and DNA. It is faster than almost all short-read aligners, yet retains unrivaled sensitivity and specificity, particularly for reads with many errors and indels. 6 413 413 25287 25287 562 562 10487 10487 172 172 3537 3537 5 5 134 134 39445 39445 1152 1152 +bcftools bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_from_vcf, bcftools_@EXECUTABLE@_to_vcf, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_plugin_@PLUGIN_ID@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@_list_samples, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@, bcftools_@EXECUTABLE@ tabular, html, fasta, txt, svg, pdf BCFtools toolkit wrappers 2015-08-12 https://samtools.github.io/bcftools/ 1.22 bcftools 1.23.1 To update Variant Analysis Variant calling, Data handling Variant calling, Data handling Genetic variation, DNA polymorphism, GWAS study, Genotyping experiment DNA polymorphism, GWAS study, Genotyping experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bcftools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bcftools bcftools BCFtools BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +bctools bctools_convert_to_binary_barcode, bctools_extract_crosslinked_nucleotides, bctools_extract_alignment_ends, bctools_extract_barcodes, bctools_merge_pcr_duplicates, bctools_remove_tail, bctools_remove_spurious_events fastq, bed bctools is a set of tools for handling barcodes and UMIs in NGS data.bctools can be used to merge PCR duplicates according to unique molecular barcodes (UMIs),to extract barcodes from arbitrary positions relative to the read starts,to clean up readthroughs into UMIs with paired-end sequencing andhandles binary barcodes as used with uvCLAP and FLASH.License: Apache License 2.0 2017-10-05 https://github.com/dmaticzka/bctools 0.2.2 bctools 0.2.2 Up-to-date Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bctools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bctools 7 124 157 1759 3227 0 0 0 0 0 0 0 0 0 0 0 0 3227 1759 157 124 +beacon2 beacon2_csv2xlsx, beacon2_pxf2bff, beacon2_vcf2bff xlsx, json beacon2-ri-tools are part of the ELIXIR-CRG Beacon v2 Reference Implementation (B2RI). 2023-08-11 https://github.com/EGA-archive/beacon2-ri-tools/tree/main 2.0.0 beacon2-ri-tools 2.1.2 To update Variant Analysis Service discovery, Database search, Genetic variation analysis Service discovery, Database search, Genetic variation analysis Genetic variation, Population genetics, Data security, Rare diseases Genetic variation, Population genetics, Data security, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beacon2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/beacon2 ga4gh_beacon GA4GH Beacon A global search engine for genetic mutations. 3 13 13 64 64 0 0 0 0 2 2 37 37 1 1 2 2 103 103 16 16 +beagle beagle vcf, txt Beagle is a program for phasing and imputing missing genotypes. 2021-07-04 https://faculty.washington.edu/browning/beagle/beagle.html 5.4_29Oct24.c8e beagle 5.4_22Jul22.46e To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/beagle /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/beagle 1 43 43 252 252 0 0 0 0 0 0 0 0 2 2 4 4 256 256 45 45 +bedops_sortbed bedops-sort-bed BEDOPS: high-performance genomic feature operations 2023-08-08 https://bedops.readthedocs.io/en/latest/ @TOOL_VERSION@ bedops 2.4.42 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedops /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bedops 1 95 95 277 277 116 116 451 451 0 0 0 0 0 0 0 0 728 728 211 211 +bedtools bedtools_annotatebed, bedtools_bamtobed, bedtools_bed12tobed6, bedtools_bedtobam, bedtools_bedtoigv, bedtools_bedpetobam, bedtools_closestbed, bedtools_clusterbed, bedtools_complementbed, bedtools_coveragebed, bedtools_expandbed, bedtools_fisher, bedtools_flankbed, bedtools_genomecoveragebed, bedtools_getfastabed, bedtools_groupbybed, bedtools_intersectbed, bedtools_jaccard, bedtools_links, bedtools_makewindowsbed, bedtools_map, bedtools_maskfastabed, bedtools_mergebed, bedtools_multicovtbed, bedtools_multiintersectbed, bedtools_nucbed, bedtools_overlapbed, bedtools_randombed, bedtools_reldistbed, bedtools_shufflebed, bedtools_slopbed, bedtools_sortbed, bedtools_spacingbed, bedtools_subtractbed, bedtools_tagbed, bedtools_unionbedgraph, bedtools_windowbed bed, bam, txt, unsorted.bam, bedgraph, fasta, html, tabular bedtools is a powerful toolset for genome arithmetic 2014-09-13 https://github.com/arq5x/bedtools2 2.31.1 bedtools 2.31.1 Up-to-date Genomic Interval Operations, Text Manipulation Mapping Mapping Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bedtools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bedtools bedtools BEDTools BEDTools is an extensive suite of utilities for comparing genomic features in BED format. https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=a018307be3563f28, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 microbiome/pathogen-detection-from-nanopore-foodborne-data 37 5261 5753 986602 1069403 7556 10120 422356 735272 1153 1223 93992 110440 336 337 10193 10644 1925759 1513143 17433 14306 +bellavista bellavista_prepare tar.gz, json Open-Source Visualization for Imaging-Based Spatial Transcriptomics 2025-05-02 https://github.com/pkosurilab/BellaVista 0.0.2 To update Single Cell, Spatial Omics, Transcriptomics, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellavista /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bellavista 1 2 2 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 +bellerophon bellerophon bam Filter mapped reads where the mapping spans a junction, retaining the 5-prime read. 2021-05-28 https://github.com/davebx/bellerophon @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bellerophon 1.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bellerophon /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bellerophon 1 350 350 2265 2265 110 110 1644 1644 41 41 843 843 0 0 0 0 4752 4752 501 501 +berokka berokka fasta, tabular Berokka is used to trim, circularise, orient & filter long read bacterial genome assemblies. 2019-03-08 https://github.com/tseemann/berokka @TOOL_VERSION@ berokka 0.2.3 To update Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/berokka /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/berokka 1 0 0 0 0 0 0 0 0 85 85 1250 1250 0 0 0 0 1250 1250 85 85 +biapy biapy yaml Accessible deep learning workflows on bioimages using BiaPy 2025-07-23 https://biapyx.github.io/ 3.6.8 To update Machine Learning, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biapy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/biapy 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +bigscape bigscape html, txt Construct sequence similarity networks of BGCs and groups them into GCF 2024-02-18 https://github.com/medema-group/BiG-SCAPE @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bigscape 2.0.3 To update Metagenomics Clustering, Global alignment, Fold recognition Clustering, Global alignment, Fold recognition Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families Phylogeny, Microbial ecology, Mapping, Metabolomics, Bioinformatics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigscape /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bigscape BiG-SCAPE BiG-SCAPE A computational framework to explore large-scale biosynthetic diversity.BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs). BiG-SCAPE does this by rapidly calculating a distance matrix between gene clusters based on a comparison of their protein domain content, order, copy number and sequence identity.It defines a distance metric between Gene Clusters using a combination of three indices (Jaccard Index of domain types, Domain Sequence Similarity the Adjacency...BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies. 1 95 95 2449 2449 0 0 0 0 0 0 0 0 0 0 0 0 2449 2449 95 95 +bigwig_outlier_bed bigwig_outlier_bed bed, txt pybigtools and numpy code to find continuous runs above a high or below a low quantile cutpoint in bigwig files 2024-07-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/bigwig_outlier_bed @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bigwig_outlier_bed /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bigwig_outlier_bed bigtools bigtools Bigtools is a library and associated tools for reading and writing bigwig and bigbed files. Rust. 1 19 19 912 912 54 54 867 867 0 0 0 0 0 0 0 0 1779 1779 73 73 +binette binette tabular Binning refinement tool 2025-01-14 https://github.com/genotoul-bioinfo/Binette @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ binette 1.2.1 To update Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binette /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/binette binette Binette Binette is a fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. 1 11 11 359 359 8 8 17 17 0 0 0 0 1 1 49 49 425 425 20 20 +binning_refiner bin_refiner tabular Reconciles the outputs of different binning programs with the aim to improve the quality of genome bins,especially with respect to contamination levels. 2022-02-18 https://github.com/songweizhi/Binning_refiner 1.4.3 binning_refiner 1.4.3 Up-to-date Metagenomics Read binning, Sequence clustering Read binning, Sequence clustering Metagenomics, Sequence assembly, Microbial ecology Metagenomics, Sequence assembly, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/binning_refiner /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/binning_refiner binning_refiner Binning_refiner Improving genome bins through the combination of different binning programs 1 64 64 236 236 0 0 0 0 0 0 0 0 0 0 0 0 236 236 64 64 +bio_hansel bio_hansel tabular Heidelberg and Enteritidis SNP Elucidation 2017-09-29 https://github.com/phac-nml/bio_hansel 2.6.1 bio_hansel 2.6.1 Up-to-date Sequence Analysis Genotyping, SNP detection, Genome assembly Genotyping, SNP detection, Genome assembly Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science Whole genome sequencing, DNA polymorphism, Genotype and phenotype, Infectious disease, Agricultural science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hansel /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hansel Biohansel BioHansel BioHansel is a tool for performing high-resolution genotyping of bacterial isolates by identifying phylogenetically informative single nucleotide polymorphisms (SNPs), also known as canonical SNPs, in whole genome sequencing (WGS) data. The application uses a fast k-mer matching algorithm to map pathogen WGS data to canonical SNPs contained in hierarchically structured schemas and assigns genotypes based on the detected SNP profile. 1 36 39 312 397 57 63 538 592 0 0 0 0 0 0 0 0 989 850 102 93 +bioext bioext_bam2msa, bioext_bealign fasta, bam A suite of Galaxy tools designed around the BioExt extension to BioPython. Align sequences, merge duplicate sequences into one, and more! 2016-11-03 https://github.com/veg/BioExt 0.21.10 python-bioext 0.21.10 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioext /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bioext 2 833 833 33209 33209 1366 1366 22291 22291 1 1 2 2 0 0 0 0 55502 55502 2200 2200 +bioinformatics_cafe fasta_regex_finder bed Miscellanea of scripts for bioinformatics 2023-01-25 https://github.com/dariober/bioinformatics-cafe/ 0.1.0 python To update Sequence Analysis mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioinformatics_cafe /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bioinformatics_cafe 1 130 130 1691 1691 126 126 1430 1430 0 0 0 0 0 0 0 0 3121 3121 256 256 +biomformat biom_add_metadata, biom_convert, biom_from_uc, biom_normalize_table, biom_subset_table, biom_summarize_table biom1, txt The biom-format package provides a command line interface and Python API for working with BIOM files. 2016-06-07 https://github.com/biocore/biom-format 2.1.17 biom-format 2.1.7 To update Metagenomics Formatting Formatting Laboratory information management, Sequence analysis Laboratory information management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biom_format /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/biom_format biomformat biomformat "This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object, as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly ""R flavor"" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods." 6 342 356 16688 16852 374 593 2736 5533 166 235 2283 2833 0 0 0 0 25218 21707 1184 882 +biotradis bacteria_tradis, tradis_essentiality, tradis_gene_insert_sites txt, tabular.gz, bam, csv, pdf Bio-Tradis is a tool suite dedicated to essentiality analyses with TraDis data. 2020-01-17 https://www.sanger.ac.uk/science/tools/bio-tradis 1.4.5 biotradis 1.4.5 Up-to-date Genome annotation Sequence analysis Sequence analysis Mobile genetic elements, Workflows Mobile genetic elements, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/biotradis /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/biotradis biotradis biotradis The Bio::TraDIS pipeline provides software utilities for the processing, mapping, and analysis of transposon insertion sequencing data. The pipeline was designed with the data from the TraDIS sequencing protocol in mind, but should work with a variety of transposon insertion sequencing protocols as long as they produce data in the expected format. 0 0 0 0 0 165 176 6369 6769 0 0 0 0 0 0 0 0 6769 6369 176 165 +biscot biscot txt, fasta, agp Bionano scaffolding correction tool 2023-01-06 https://github.com/institut-de-genomique/biscot 2.3.3 biscot 2.3.3 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/biscot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/biscot 1 2 2 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 2 2 +blastxml_to_gapped_gff3 blastxml_to_gapped_gff3 gff3 BlastXML to gapped GFF3 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/blastxml_to_gapped_gff3 1.1 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/blastxml_to_gapped_gff3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/blastxml_to_gapped_gff3 1 121 128 908 952 69 77 156 193 18 18 185 185 0 0 0 0 1330 1249 223 208 +bmtagger bmtagger remove contaminant reads 2025-11-12 https://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bmtagger 3.101 To update Metagenomics Data filtering, Read pre-processing Read pre-processing Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bmtagger /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bmtagger bmtagger bmtagger Best Match Tagger for removing contaminant reads from metagenomics datasets 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +bowtie2 bowtie2 bam, txt Bowtie2: Fast and sensitive read alignment 2017-05-08 http://bowtie-bio.sourceforge.net/bowtie2 2.5.5 bowtie2 2.5.5 Up-to-date Next Gen Mappers Read mapping Read mapping Mapping, Genomics, Mapping Mapping, Genomics, Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bowtie2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bowtie2 bowtie2 Bowtie 2 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=63478edcea3f449a, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 microbiome/metagenomics-assembly 1 14402 16726 416270 533359 34023 59018 582611 1027362 4158 5085 66910 84030 1570 1574 28821 28955 1673706 1094612 82403 54153 +bp_genbank2gff3 bp_genbank2gff3 gff3 Converts GenBank format files to GFF3 2015-08-14 https://bioperl.org/ 1.1 perl-bioperl 1.7.8 To update Sequence Analysis Data handling, Service invocation Data handling, Service invocation Genomics, Software engineering, Data management Genomics, Software engineering iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bioperl /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bioperl bioperl BioPerl A collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It provides software modules for many of the typical tasks of bioinformatics programming. 1 638 721 10572 11606 974 1075 10887 11385 180 207 8997 9165 22 22 309 309 32465 30765 2025 1814 +bracken est_abundance tabular, txt Bayesian Reestimation of Abundance with KrakEN 2019-10-15 https://github.com/jenniferlu717/Bracken/releases 3.1 bracken 3.1p1 To update Sequence Analysis, Metagenomics Statistical calculation Statistical calculation Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bracken /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bracken bracken Bracken Bracken is a companion program to Kraken 1, KrakenUniq, or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample). https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=b14845359b702444 microbiome/taxonomic-profiling 1 1714 1714 108307 108307 804 804 27569 27569 265 265 8873 8873 59 59 12432 12432 157181 157181 2842 2842 +breseq breseq html, tabular, zip, txt, phylip Predicts mutations in microbial genomes 2019-10-21 https://github.com/barricklab/breseq 0.35.5 breseq 0.40.1 To update Variant Analysis Polymorphism detection Polymorphism detection Sequencing, Sequence analysis, DNA mutation Sequencing, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/breseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/breseq breseq breseq Runs Breseq software on a set of fastq files. 1 198 198 4455 4455 0 0 0 0 71 83 896 1004 0 0 0 0 5459 5351 281 269 +brew3r_r brew3r_r gtf, tabular Extend 3' end of a GTF using another GTF as a template 2024-06-11 https://bioconductor.org/packages/release/bioc/html/BREW3R.r.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ To update Transcriptomics, RNA Genome annotation Genome annotation Transcriptomics, Genomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/brew3r_r /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/brew3r_r brew3r.r BREW3R.r This R package provide functions that are used in the BREW3R workflow. This mainly contains a function that extend a gtf as GRanges using information from another gtf (also as GRanges). The process allows to extend gene annotation without increasing the overlap between gene ids. 1 5 5 75 75 4 4 22 22 0 0 0 0 0 0 0 0 97 97 9 9 +busco busco txt, tabular, png, gff3, fasta BUSCO assess genome and annotation completeness 2017-01-12 https://gitlab.com/ezlab/busco/-/releases 5.8.0 busco 6.1.0 To update Sequence Analysis, Genome annotation Sequence assembly validation Sequence assembly validation Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/busco /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/busco busco BUSCO Provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 1 5636 5838 134029 137202 5194 5212 58403 58497 3096 3288 49227 52147 262 262 8860 8866 256712 250519 14600 14188 +bwa bwa_mem, bwa bam Wrapper for bwa mem, aln, sampe, and samse 2017-11-21 http://bio-bwa.sourceforge.net/ 0.7.19 bwa 0.7.19 Up-to-date Next Gen Mappers Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Genome indexing, Sequence alignment, Read mapping, Sequence alignment, Generation, Sequence alignment, Generation, Sequence alignment, Sequence alignment Mapping Mapping devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bwa bwa BWA Fast, accurate, memory-efficient aligner for short and long sequencing reads https://usegalaxy.eu/published/workflow?id=6223333100a9e73f 2 11730 13297 948091 1092022 23003 36519 419994 745074 3413 4520 101030 123169 314 317 6918 7008 1967273 1476033 54653 38460 +bwa_mem2 bwa_mem2_idx, bwa_mem2 bwa_mem2_index, bam Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. 2021-10-08 https://github.com/bwa-mem2/bwa-mem2 2.3 bwa-mem2 2.3 Up-to-date Next Gen Mappers Sequence alignment Sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwa_mem2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bwa_mem2 bwa-mem2 Bwa-mem2 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. https://usegalaxy.eu/published/workflow?id=8edf456f4aeddaac, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 2 4165 4165 95467 95467 4910 4910 69756 69756 1058 1058 31125 31125 67 67 578 578 196926 196926 10200 10200 +bwameth bwameth bam Fast and accurate alignment of BS-seq reads 2016-09-14 https://github.com/brentp/bwa-meth @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bwameth 0.2.9 To update Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/bwameth /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/bwameth 1 691 1020 10937 16134 862 907 12645 13009 176 176 1696 1700 2 2 2 2 30845 25280 2105 1731 +cactus cactus_cactus, cactus_export h5, gfa2.gz, maf, vg, tar Cactus is a reference-free whole-genome multiple alignment program 2022-01-28 https://github.com/ComparativeGenomicsToolkit/cactus 2.7.1 To update Sequence Analysis Multiple sequence alignment, Genome alignment Multiple sequence alignment, Genome alignment Genomics, Sequence analysis, Phylogeny, Sequence assembly, Mapping, Phylogenetics Genomics, Sequence assembly, Mapping, Phylogenetics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/cactus /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cactus cactus Cactus Cactus is a reference-free whole-genome multiple alignment program. 2 92 92 575 575 0 0 0 0 96 96 2883 2883 4 4 12 12 3470 3470 192 192 +calculate_contrast_threshold calculate_contrast_threshold txt Calculates a contrast threshold from the CDT file generated by ``tag_pileup_frequency``. The calculated values are then used to set a uniform contrast for all the heatmaps generated downstream. 2019-08-26 https://github.com/CEGRcode/ChIP-QC-tools/tree/master/calculate_contrast_threshold 1.0.0 numpy To update Visualization, Genomic Interval Operations, SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_contrast_threshold /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/calculate_contrast_threshold 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +calculate_numeric_param calculate_numeric_param Calculate a numeric parameter value using integer and float values. 2021-05-04 0.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/calculate_numeric_param /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/calculate_numeric_param 1 21 21 2700 2700 7 7 379 379 0 0 0 0 0 0 0 0 3079 3079 28 28 +cami_amber biobox_add_taxid, cami_amber, cami_amber_add, cami_amber_convert tabular, html Evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments 2024-05-20 https://github.com/CAMI-challenge/AMBER 2.0.7 cami-amber 2.0.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cami_amber /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cami_amber cami-amber AMBER AMBER is an evaluation package for the comparative assessment of genome reconstructions and taxonomic assignments from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects. The provided metrics were used in the first community benchmarking challenge of the initiative for the Critical Assessment of Metagenomic Interpretation. 4 8 8 10522 10522 0 0 0 0 0 0 0 0 0 0 0 0 10522 10522 8 8 +cawlign cawlign fasta Codon-aware alignment of sequences to a reference. 2025-09-30 https://github.com/veg/cawlign 0.1.15 cawlign 0.1.16 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/cawlign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cawlign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +cd_hit cd_hit txt, fasta Cluster or compare biological sequence datasets 2018-02-26 http://weizhongli-lab.org/cd-hit/ 4.8.1 cd-hit 4.8.1 Up-to-date Sequence Analysis, Fasta Manipulation Sequence clustering Sequence clustering Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cdhit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cdhit cd-hit cd-hit Cluster a nucleotide dataset into representative sequences. 1 899 899 20148 20148 1 1 2 2 1 1 2 2 57 57 1174 1174 21326 21326 958 958 +celltypist celltypist h5ad, png, pdf, svg CellTypist – Automated cell type annotation for scRNA-seq datasets 2026-03-10 https://www.celltypist.org/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ celltypist 1.7.1 To update Single Cell, Spatial Omics, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/celltypist /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/celltypist celltypist celltypist A tool for semi-automatic cell type classification 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +cemitool cemitool tabular, txt, html Gene co-expression network analysis tool 2022-10-10 https://www.bioconductor.org/packages/release/bioc/html/CEMiTool.html 1.34.0 bioconductor-cemitool 1.34.0 Up-to-date Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Pathway or network analysis Enrichment analysis, Pathway or network analysis Gene expression, Transcriptomics, Microarray experiment Transcriptomics, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cemitool /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cemitool cemitool CEMiTool It unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network. 1 45 45 354 354 87 87 584 584 6 6 154 154 0 0 0 0 1092 1092 138 138 +charts charts tabular Enables advanced visualization options in Galaxy Charts 2018-01-30 https://github.com/galaxyproject/tools-iuc/tree/master/tools/charts/ 1.0.1 r-getopt To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/charts /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/charts 0 2016 2636 4166 5631 3945 8272 8242 16754 8 145 13 350 58 58 111 111 22846 12532 11111 6027 +checkm checkm_analyze, checkm_lineage_set, checkm_lineage_wf, checkm_plot, checkm_qa, checkm_taxon_set, checkm_taxonomy_wf, checkm_tetra, checkm_tree, checkm_tree_qa tabular, zip, fasta, phyloxml, json, newick Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes 2022-07-29 https://github.com/Ecogenomics/CheckM 1.2.5 checkm-genome 1.2.5 Up-to-date Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/checkm checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. microbiome/metagenomics-binning 10 717 717 12189 12189 179 179 1510 1510 96 96 2254 2254 50 50 1469 1469 17422 17422 1042 1042 +checkm2 checkm2 tabular Rapid assessment of genome bin quality using machine learning 2024-11-08 https://github.com/chklovski/CheckM2 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ checkm2 1.1.0 To update Metagenomics Sequence assembly validation, Validation, Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence assembly validation, Sequence composition calculation, Statistical calculation Genomics, Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management Phylogenomics, Phylogenetics, Taxonomy, Metagenomics, Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/checkm2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/checkm2 checkm CheckM CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. 1 228 228 1602 1602 187 187 1322 1322 0 0 0 0 15 15 1268 1268 4192 4192 430 430 +cherri cherri_eval, cherri_train csv, tgz Computational Help Evaluating RNA-RNA interactions 2022-12-09 https://github.com/BackofenLab/Cherri 0.7 cherri 0.8 To update Transcriptomics, RNA Molecular interactions, pathways and networks, Structure analysis, Machine learning Molecular interactions, pathways and networks, Structure analysis, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cherri /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cherri cherri cherri CheRRI detects functional RNA-RNA interaction (RRI) sites, by evaluating if an interaction site most likely occurs in nature. It helps to filter interaction sites generated either experimentally or by an RRI prediction algorithm by removing false positive interactions. 2 1 1 207 207 0 0 0 0 0 0 0 0 0 0 0 0 207 207 1 1 +chewbbaca chewbbaca_allelecall, chewbbaca_allelecallevaluator, chewbbaca_createschema, chewbbaca_downloadschema, chewbbaca_extractcgmlst, chewbbaca_joinprofiles, chewbbaca_nsstats, chewbbaca_prepexternalschema fasta, html, tabular, zip, txt BSR-Based Allele Calling Algorithm 2024-04-13 https://github.com/B-UMMI/chewBBACA/tree/master 3.3.10 chewbbaca 3.5.4 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chewbbaca /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chewbbaca 8 100 100 9644 9644 0 0 0 0 0 0 0 0 0 0 0 0 9644 9644 100 100 +chira chira_collapse, chira_extract, chira_map, chira_merge, chira_quantify fasta, tabular, bed Chimeric Read Annotator for RNA-RNA interactome data 2020-01-19 https://github.com/pavanvidem/chira 1.4.3 chira 1.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis RNA, Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA Molecular interactions, pathways and networks, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chira /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chira chira ChiRA ChiRA is a tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc. 5 128 137 39830 42352 95 95 21742 21742 17 17 585 585 0 0 0 0 64679 62157 249 240 +chopin2 chopin2 tabular Domain-Agnostic Supervised Learning with Hyperdimensional Computing 2023-01-18 https://github.com/cumbof/chopin2 1.0.9.post1 chopin2 To update Machine Learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopin2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chopin2 1 0 0 0 0 8 8 21 21 0 0 0 0 0 0 0 0 21 21 8 8 +chopper chopper Filtering and trimming of fastq files with long read sequencing such as PacBio or ONT. 2025-07-22 https://github.com/wdecoster/chopper @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ chopper 0.13.0 To update Sequence Analysis, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chopper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chopper 1 6 6 10 10 0 0 0 0 0 0 0 0 0 0 0 0 10 10 6 6 +chromap chromap bed, txt Fast alignment and preprocessing of chromatin profiles. 2026-02-17 https://github.com/haowenz/chromap 0.3.2 chromap 0.3.2 Up-to-date Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chromap 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +chromeister chromeister txt, png, csv ultra-fast pairwise genome comparisons 2020-09-30 https://github.com/estebanpw/chromeister @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ chromeister 1.5.a To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/chromeister /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/chromeister 1 550 550 10141 10141 0 0 0 0 277 277 1883 1883 56 56 2443 2443 14467 14467 883 883 +cialign cialign fasta, txt, png, tsv Tool to clean, visualise and analyse a multiple sequence alignment 2025-08-04 https://github.com/KatyBrown/CIAlign 1.1.4 cialign 1.1.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cialign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cialign 1 3 3 6 6 0 0 0 0 0 0 0 0 0 0 0 0 6 6 3 3 +circexplorer2 circexplorer2 tgz, bigwig, bed, tabular Comprehensive and integrative circular RNA analysis toolset. 2022-08-26 https://github.com/YangLab/CIRCexplorer2 2.3.8 circexplorer2 2.3.8 Up-to-date RNA, Assembly RNA splicing, Gene transcripts, Literature and language RNA splicing, Gene transcripts, Literature and language iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/circexplorer2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/circexplorer2 circexplorer2 CIRCexplorer2 Genome-wide annotation of circRNAs and their alternative back-splicing/splicing. 1 39 39 833 833 0 0 0 0 0 0 0 0 0 0 0 0 833 833 39 39 +circos circos_aln_to_links, circos_binlinks, circos_bundlelinks, circos, circos_gc_skew, circos_resample, circos_wiggle_to_scatter, circos_wiggle_to_stacked, circos_tableviewer, circos_interval_to_text, circos_interval_to_tile tabular, png, svg, tar.gz, bigwig Build Circos Plots in Galaxy 2017-08-07 http://circos.ca/ 0.69.8 circos 0.69.9 To update Graphics Sequence visualisation Sequence visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/circos /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/circos galactic_circos Galactic Circos Galactic Circos is a Galaxy wrapper providing a GUI for the Circos tool. Circos allows visualizing data in a circular format. 11 1387 1476 30286 32934 1656 1808 33780 36943 409 515 10963 28143 24 25 586 588 98608 75615 3824 3476 +cite_seq_count cite_seq_count yaml, tsv, mtx Count CMO/HTO 2023-01-18 https://github.com/Hoohm/CITE-seq-Count @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ cite-seq-count 1.4.5 To update Single Cell, Transcriptomics, Proteomics RNA-Seq quantification RNA-Seq quantification Transcriptomics, Immunoproteins and antigens Transcriptomics, Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cite_seq_count /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cite_seq_count CITE-seq-Count CITE-seq-Count Tool for counting antibody TAGS from a CITE-seq and/or cell hashing experiment. 1 5 5 23 23 6 6 21 21 1 1 290 290 0 0 0 0 334 334 12 12 +clair3 clair3 vcf_bgzip Symphonizing pileup and full-alignment for high-performance long-read variant calling 2022-06-15 https://github.com/HKU-BAL/Clair3 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ clair3 2.0.1 To update Sequence Analysis, Variant Analysis Variant calling Variant calling Molecular genetics Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clair3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/clair3 clair3 Clair3 Clair3 is a germline small variant caller for long-reads. Clair3 makes the best of two major method categories: pileup calling handles most variant candidates with speed, and full-alignment tackles complicated candidates to maximize precision and recall. Clair3 runs fast and has superior performance, especially at lower coverage. Clair3 is simple and modular for easy deployment and integration. microbiome/pathogen-detection-from-nanopore-foodborne-data 1 328 328 5269 5269 52 52 1858 1858 13 13 246 246 2 2 54 54 7427 7427 395 395 +clustalw clustalw clustal, nhx ClustalW multiple sequence alignment program for DNA or proteins 2022-10-02 http://www.clustal.org/clustal2/ 2.1 clustalw 2.1 Up-to-date Phylogenetics, Sequence Analysis Multiple sequence alignment Multiple sequence alignment Phylogeny, Sequence analysis Phylogeny, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustalw /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/clustalw clustal2 Clustal 2 (Clustal W, Clustal X) Multiple sequence alignment program with a command-line interface (Clustal W) and a graphical user interface (Clustal X). The display colours allow conserved features to be highlighted for easy viewing in the alignment. It is available for several platforms, including Windows, Macintosh PowerMac, Linux and Solaris.Names occassionally spelled also as Clustal W2, ClustalW2, ClustalW, ClustalX, Clustal2. microbiome/pathogen-detection-from-nanopore-foodborne-data 1 2268 2506 114395 117339 3966 8263 54653 99642 837 966 11073 13924 42 43 726 730 231635 180847 11778 7113 +clustering_from_distmat clustering_from_distmat newick, tabular Distance matrix-based hierarchical clustering using SciPy 2024-08-08 https://github.com/galaxyproject/tools-iuc/tree/master/tools/clustering_from_distmat/ 1.1.1 python To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/clustering_from_distmat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/clustering_from_distmat 1 69 69 305 305 0 0 0 0 0 0 0 0 0 0 0 0 305 305 69 69 +cnv-vcf2json cnv_vcf2json json cnv-vcf2json Converts structural variants VCF file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 2.0.0 cnv-vcf2json To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-vcf2json /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cnv-vcf2json 1 11 11 69 69 0 0 0 0 1 1 12 12 0 0 0 0 81 81 12 12 +cnv_phenopacket cnv_phenopacket json cnv-phenopacket Converts TSV metadata file to JSON. 2024-02-27 https://pypi.org/project/cnv-phenopacket/ 1.0.2 cnv-phenopacket To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnv-phenopacket /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cnv-phenopacket 1 7 7 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 7 7 +cnvkit cnvkit_access, cnvkit_antitarget, cnvkit_autobin, cnvkit_batch, cnvkit_export_bed, cnvkit_breaks, cnvkit_call, cnvkit_export_cdt, cnvkit_coverage, cnvkit_diagram, cnvkit_fix, cnvkit_genemetrics, cnvkit_heatmap, cnvkit_export_jtv, cnvkit_export_nexus_basic, cnvkit_export_nexus_ogt, cnvkit_reference, cnvkit_scatter, cnvkit_export_seg, cnvkit_segment, cnvkit_segmetrics, cnvkit_sex, cnvkit_target, cnvkit_theta, cnvkit_export_vcf bed, cns, cnn, cnr, pdf, png, txt, cdt, jtv, tabular, seg, vcf detecting copy number variants and alterations genome-wide from high-throughput sequencing 2023-03-14 https://github.com/etal/cnvkit 0.9.12 cnvkit 0.9.13 To update Variant Analysis Variant calling Variant calling DNA structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cnvkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cnvkit cnvkit CNVkit CNVkit is a software toolkit to infer and visualize copy number from targeted DNA sequencing data. 25 59 59 3401 3401 0 0 0 0 3 3 430 430 0 0 0 0 3831 3831 62 62 +codeml codeml txt Detects positive selection 2017-07-19 http://abacus.gene.ucl.ac.uk/software/paml.html 4.9 paml 4.10.10 To update Phylogenetics Probabilistic sequence generation, Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree analysis Probabilistic sequence generation Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/codeml /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/codeml paml PAML Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. 1 72 84 62891 63000 0 0 0 0 0 0 0 0 0 0 0 0 63000 62891 84 72 +cojac cooc_mutbamscan, cooc_pubmut, cooc_tabmut yaml, json, tabular, tsv, csv, html co-occurrence of mutations on amplicons 2022-08-11 https://github.com/cbg-ethz/cojac 0.9.3 cojac 0.9.3 Up-to-date Metagenomics, Sequence Analysis Genetic variation Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cojac /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cojac cojac COJAC CoOccurrence adJusted Analysis and Calling - The cojac package comprises a set of command-line tools to analyse co-occurrence of mutations on amplicons. It is useful, for example, for early detection of viral variants of concern (e.g. Alpha, Delta, Omicron) in environmental samples, and has been designed to scan for multiple SARS-CoV-2 variants in wastewater samples, as analyzed jointly by ETH Zurich, EPFL and Eawag. 3 13 13 2763 2763 7 7 20 20 0 0 0 0 0 0 0 0 2783 2783 20 20 +colabfold colabfold_alphafold, colabfold_msa colab.tar Protein prediction based on AlphaFold2 2024-03-24 https://github.com/sokrypton/ColabFold 1.5.5 To update Proteomics, Graphics Database search, Protein structure prediction, Fold recognition Database search, Protein structure prediction, Fold recognition Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics Protein folds and structural domains, Protein folding, stability and design, Structure prediction, Sequence sites, features and motifs, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/colabfold /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/colabfold Colabfold ColabFold ColabFold databases are MMseqs2 expandable profile databases to generate diverse multiple sequence alignments to predict protein structures. 2 0 0 0 0 233 233 10606 10606 0 0 0 0 0 0 0 0 10606 10606 233 233 +colibread commet, discosnp_rad, discosnp_pp, kissplice, lordec, mapsembler2, takeabreak csv, png, vcf, fasta, tabular Colib'read tools are all dedicated to the analysis of NGS datasets without the need of any reference genome 2017-10-02 https://colibread.inria.fr/ @TOOL_VERSION@ commet 24.7.14 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/colibread /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/colibread 7 47 52 1393 1457 0 0 0 0 0 0 0 0 68 68 259 262 1719 1652 120 115 +collection_column_join collection_column_join tabular, txt Column Join on Collections 2016-05-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/collection_column_join 0.0.3 coreutils 8.25 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_column_join /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/collection_column_join https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 microbiome/metagenomics-assembly, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 4863 5343 27514 31287 5333 6304 23001 29705 862 938 3486 4038 891 892 5039 5055 70085 59040 13477 11949 +collection_element_identifiers collection_element_identifiers txt Extract element identifiers of a collection 2018-06-13 https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers 0.0.3 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/collection_element_identifiers /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/collection_element_identifiers https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=5d401d357500617f, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b1f68ff8158d0b85, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809 microbiome/dada-16S, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 2213 2274 12646 13068 2624 2659 10358 10479 367 368 1829 1840 308 308 3128 3128 28515 27961 5609 5512 +column_maker Add_a_column1 Compute an expression on every row 2019-06-24 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_maker 2.1 python To update Text Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_maker /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/column_maker https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 microbiome/dada-16S, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 6569 7917 2959895 3934273 6681 15326 265585 753337 1099 1306 98471 100332 253 259 11349 11525 4799467 3335300 24808 14602 +column_order_header_sort column_order_header_sort tabular Sort Column Order by heading 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_order_header_sort 0.0.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_order_header_sort /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/column_order_header_sort 1 291 369 4668 5579 342 434 1768 2044 0 0 0 0 13 13 21 21 7644 6457 816 646 +column_remove_by_header column_remove_by_header tabular Remove columns by header 2017-04-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/column_remove_by_header 1.0 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/column_remove_by_header /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/column_remove_by_header https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809 1 787 891 9614 10501 815 908 5129 5911 48 48 2147 2147 46 46 219 219 18778 17109 1893 1696 +comebin comebin Binning of metagenomic contigs using COntrastive Multi-viEw representation learning 2025-07-03 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/comebin 1 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 +comebin_bam comebin_bam bam Generate bam file for COMEBin 2025-11-07 https://github.com/ziyewang/COMEBin 1.0.4 comebin 1.0.4 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/comebin_bam/ /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/comebin_bam 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +compleasm compleasm tsv, gff3, fasta, txt Compleasm: a faster and more accurate reimplementation of BUSCO 2023-12-04 https://github.com/huangnengCSU/compleasm 0.2.6 compleasm 0.2.8 To update Sequence Analysis Sequence assembly validation Sequence assembly validation Sequence assembly, Genomics, Transcriptomics, Sequence analysis Sequence assembly, Transcriptomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compleasm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/compleasm compleasm Compleasm Compleasm: a faster and more accurate reimplementation of BUSCO.It provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs. 1 99 99 675 675 92 92 638 638 20 20 269 269 18 18 449 449 2031 2031 229 229 +compose_text_param compose_text_param Compose a text parameter value using text, integer and float values 2019-05-09 0.1.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compose_text_param /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/compose_text_param https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646 microbiome/pathogen-detection-from-nanopore-foodborne-data 1 939 944 51227 51246 555 555 20402 20402 142 142 1655 1655 14 14 2809 2809 76112 76093 1655 1650 +compress_file compress_file gz Compress files. 2022-02-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/compress_file 0.1.0 gzip To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/compress_file /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/compress_file 1 439 439 10916 10916 523 523 7826 7826 101 101 13887 13887 0 0 0 0 32629 32629 1063 1063 +concoct concoct, concoct_coverage_table, concoct_cut_up_fasta, concoct_extract_fasta_bins, concoct_merge_cut_up_clustering csv, txt, tabular, fasta, bed CONCOCT (Clustering cONtigs with COverage and ComposiTion) does unsupervised binning of metagenomic contigs byusing nucleotide composition - kmer frequencies - and coverage data for multiple samples. CONCOCT can accurately(up to species level) bin metagenomic contigs. 2022-02-18 https://github.com/BinPro/CONCOCT 1.1.0 concoct 1.1.0 Up-to-date Metagenomics Sequence clustering, Read binning Sequence clustering, Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/concoct /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/concoct concoct CONCOCT A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. 5 107 107 9955 9955 19 19 187 187 0 0 0 0 4 4 3085 3085 13227 13227 130 130 +constava constava csv Calculate 'conformational states probabilities' and 'conformational state variability' from a protein structure ensemble 2024-08-13 https://github.com/bio2byte/constava 1.2.0 constava 1.2.0 Up-to-date Statistics, Proteomics Protein geometry calculation Protein geometry calculation Protein folding, stability and design Protein folding, stability and design iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/constava /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/constava constava Constava Constava calculates conformational states probability and conformational state variability from protein structure ensembles. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +contig_annotation_tool cat_add_names, cat_bins, cat_contigs, cat_prepare, cat_summarise tabular, txt Contig Annotation Tool (CAT) 2019-11-27 https://github.com/dutilh/CAT 5.2.3 cat 6.0.1 To update Metagenomics Taxonomic classification, Sequence assembly, Coding region prediction Taxonomic classification, Sequence assembly, Coding region prediction Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly Metagenomics, Metagenomic sequencing, Taxonomy, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cat cat_bins CAT and BAT Contig Annotation Tool (CAT) and Bin Annotation Tool (BAT) are pipelines for the taxonomic classification of long DNA sequences and metagenome assembled genomes (MAGs/bins) of both known and (highly) unknown microorganisms, as generated by contemporary metagenomics studies. The core algorithm of both programs involves gene calling, mapping of predicted ORFs against the nr protein database, and voting-based classification of the entire contig / MAG based on classification of the individual ORFs. 5 257 267 17418 17676 216 231 1590 1750 84 85 848 875 0 0 0 0 20301 19856 583 557 +control_freec control_freec tabular, txt, bed, png Control-FREEC is a tool for detection of copy-number changes and allelic imbalances (including LOH) using deep-sequencing data originally developed by the Bioinformatics Laboratory of Institut Curie (Paris). It automatically computes, normalizes, segments copy number and beta allele frequency (BAF) profiles, then calls copy number alterations and LOH. 2020-07-22 http://boevalab.inf.ethz.ch/FREEC/ 11.6 gawk To update Variant Analysis Copy number estimation, Variant calling, Genome alignment Copy number estimation, Variant calling, Genome alignment DNA structural variation, Oncology, Human genetics, Data mining Oncology, Human genetics, Data mining iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/freec /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/freec freec FREEC A tool for control-free copy number alteration (CNA) and allelic imbalances (LOH) detection using deep-sequencing data, particularly useful for cancer studies. 1 118 118 1565 1575 0 0 0 0 4 4 201 201 1 1 17 17 1793 1783 123 123 +coreprofiler coreprofiler_allele_calling tabular, json, fasta, tsv CoreProfiler, a tool for cgMLST allele calling from bacterial genome assemblies 2025-07-22 https://gitlab.com/ifb-elixirfr/abromics/coreprofiler 2.0.0 coreprofiler 2.0.0 Up-to-date Variant Analysis Multilocus sequence typing Multilocus sequence typing Microbiology, Bioinformatics, Phylogenetics Microbiology, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coreprofiler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/coreprofiler coreprofiler CoreProfiler CoreProfiler is a cgMLST (core genome multilocus sequence typing) software that identifies alleles in bacterial genome assemblies by comparing them to a reference allele scheme. It detects both exact matches to known alleles and potential novel alleles using a two-step BLAST-based approach, enabling robust and reproducible strain genotyping. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +cosg cosg tabular Marker gene identification for single-cell sequencing data using COSG. 2024-05-29 https://github.com/genecell/COSG 1.0.1 cosg 1.0.4 To update Transcriptomics, Sequence Analysis, Single Cell Nucleic acid sequence analysis Nucleic acid sequence analysis Bioinformatics Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cosg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cosg cosg COSG COSG is a cosine similarity-based method for more accurate and scalable marker gene identification. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +coverage_report CoverageReport2 pdf Generate Detailed Coverage Report from BAM file 2017-10-16 https://github.com/galaxyproject/tools-iuc 0.0.5 perl-number-format 1.76 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverage_report /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/coverage_report 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +coverm coverm_contig, coverm_genome tabular CoverM genome and contig wrappers 2022-04-26 https://github.com/wwood/CoverM 0.7.0 coverm 0.7.0 Up-to-date Sequence Analysis Local alignment Local alignment Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/coverm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/coverm coverm CoverM Read coverage calculator for metagenomics microbiome/metagenomics-assembly 2 147 147 3594 3594 14 14 414 414 11 11 125 125 7 7 565 565 4698 4698 179 179 +cramino cramino binary, txt A tool for quick quality assessment of cram and bam files, intended for long read sequencing. 2025-06-17 https://github.com/wdecoster/cramino @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ cramino 1.3.0 To update Statistics, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cramino /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cramino 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +craq craq Assess the accuracy of assembled genomic sequences 2026-03-18 https://github.com/JiaoLaboratory/CRAQ 1.10 craq 1.10 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/craq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/craq 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +crispr_studio crispr_studio tabular, svg CRISPR Studio is a program developed to facilitate and accelerate CRISPR array visualization. 2019-08-13 https://github.com/moineaulab/CRISPRStudio 1 crispr_studio 1 Up-to-date Sequence Analysis Visualisation Visualisation Sequence analysis, Genomics, Data visualisation Sequence analysis, Genomics, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crispr_studio /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/crispr_studio crisprstudio CRISPRStudio CRISPRStudio is a program developed to facilitate and accelerate CRISPR array visualization. It works by first comparing spacers sequence homology in a dataset, then assigning a two-color-code to each cluster of spacers and finally writing an svg file, which can be opened in graphics vector editor. 1 94 103 2795 2880 0 0 0 0 0 0 0 0 0 0 0 0 2880 2795 103 94 +crosscontamination_barcode_filter crosscontamination_barcode_filter pdf, tabular Barcode contamination discovery tool 2018-07-27 https://github.com/galaxyproject/tools-iuc/tree/master/tools/crosscontamination_barcode_filter @VERSION@ r-ggplot2 2.2.1 To update Transcriptomics, Visualization, Single Cell Filtering, Sequence contamination filtering, Sequencing quality control, RNA-Seq analysis Filtering, Sequence contamination filtering, RNA-Seq analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crosscontamination_barcode_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/crosscontamination_barcode_filter cross-contamination_barcode_filter Cross-contamination Barcode Filter This tool produces plots enabling the discovery of cross-contamination of samples across the full selection of barcodes used in a sequencing plate. It also filters false barcodes from each batch and retains only the 'real' barcodes. 1 68 99 146 415 48 49 82 144 0 0 0 0 0 0 0 0 559 228 148 116 +crossmap crossmap_bam, crossmap_bed, crossmap_bw, crossmap_gff, crossmap_region, crossmap_vcf, crossmap_wig bam, bed, bigwig, gff, vcf, bedgraph CrossMap converts genome coordinates or annotation files between genome assemblies 2016-04-04 http://crossmap.sourceforge.net/ 0.7.3 crossmap 0.7.3 Up-to-date Convert Formats, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/crossmap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/crossmap 7 84 104 2277 2776 222 254 4500 5654 0 0 0 0 0 0 0 0 8430 6777 358 306 +cuffcompare cuffcompare txt, tabular, gtf Galaxy wrappers for the Cuffcompare tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffcompare /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cuffcompare 1 177 329 710 1264 569 5791 1726 25159 29 98 186 496 65 66 294 329 27248 2916 6284 840 +cuffdiff cuffdiff tabular, txt, sqlite Galaxy wrappers for the Cuffdiff tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffdiff /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cuffdiff 1 567 854 3184 6491 3733 20588 18787 118461 6 616 28 4231 1 1 4 4 129187 22003 22059 4307 +cufflinks cufflinks tabular, gtf, txt Galaxy wrappers for the Cufflinks tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cufflinks /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cufflinks https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646 1 893 1397 24563 35224 5434 27612 57968 356362 281 854 2678 10520 43 47 977 1058 403164 86186 29910 6651 +cuffmerge cuffmerge gtf Galaxy wrappers for the Cuffmerge tool. 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffmerge /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cuffmerge 1 355 714 2092 3626 2472 13902 16686 68295 96 573 635 3101 57 57 128 128 75150 19541 15246 2980 +cuffnorm cuffnorm tabular, txt The Cuffnorm tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffnorm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cuffnorm 1 66 117 302 707 202 1179 713 13525 49 71 287 367 0 0 0 0 14599 1302 1367 317 +cuffquant cuffquant cxb The Cuffquant tool 2020-06-08 http://cole-trapnell-lab.github.io/cufflinks/ 2.2.1 cufflinks 2.2.1 Up-to-date Transcriptomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/cufflinks/cuffquant /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/cufflinks/cuffquant 1 49 79 352 767 192 1326 1070 15964 22 47 257 426 0 0 0 0 17157 1679 1452 263 +cutadapt cutadapt fastqsanger, txt, json Flexible tool to remove adapter sequences (and quality trim) high throughput sequencing reads (fasta/fastq). 2018-02-20 https://cutadapt.readthedocs.org/en/stable/ 5.2 cutadapt 5.2 Up-to-date Fasta Manipulation, Fastq Manipulation, Sequence Analysis Sequence trimming, Primer removal, Read pre-processing Sequence trimming, Primer removal, Read pre-processing Genomics, Probes and primers, Sequencing Genomics, Probes and primers, Sequencing lparsons https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutadapt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cutadapt cutadapt Cutadapt Find and remove adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 1 14131 16253 330892 364942 22476 26008 409500 482165 4256 4631 79748 86014 1579 1582 59464 59550 992671 879604 48474 42442 +cutesv cutesv vcf Long-read sequencing enables the comprehensive discovery of structural variations (SVs). However, it is still non-trivial to achieve high sensitivity and performance simultaneously due to the complex SV characteristics implied by noisy long reads. Therefore, we propose cuteSV, a sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection. Benchmarks on real Pacific Biosciences (PacBio) and Oxford Nanopore Technology (ONT) datasets demonstrate that cuteSV has better yields and scalability than state-of-the-art tools. 2020-09-23 https://github.com/tjiangHIT/cuteSV 2.1.3 cutesv 2.1.3 Up-to-date Variant Analysis Split read mapping, Genotyping, Structural variation detection Split read mapping, Genotyping, Structural variation detection DNA structural variation, Sequencing, Computer science Sequencing, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cutesv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cutesv cuteSV cuteSV Long Read based Human Genomic Structural Variation Detection with cuteSV | Long-read sequencing technologies enable to comprehensively discover structural variations (SVs). However, it is still non-trivial for state-of-the-art approaches to detect SVs with high sensitivity or high performance or both. Herein, we propose cuteSV, a sensitive, fast and lightweight SV detection approach. cuteSV uses tailored methods to comprehensively collect various types of SV signatures, and a clustering-and-refinement method to implement a stepwise SV detection, which enables to achieve high sensitivity without loss of accuracy. Benchmark results demonstrate that cuteSV has better yields on real datasets. Further, its speed and scalability are outstanding and promising to large-scale data analysis 1 58 58 344 344 0 0 0 0 11 11 166 166 0 0 0 0 510 510 69 69 +cwpair2 cwpair2 tabular Contains a tool that takes a list of called peaks on both strands and produces a list of matched pairsand a list of unmatched orphans. 2015-12-18 1.1.1 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cwpair2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cwpair2 1 0 0 0 0 33 85 60 283 0 0 0 0 0 0 0 0 283 60 85 33 +dada2 dada2_assignTaxonomyAddspecies, dada2_dada, dada2_filterAndTrim, dada2_learnErrors, dada2_makeSequenceTable, dada2_mergePairs, dada2_plotComplexity, dada2_plotQualityProfile, dada2_primerCheck, dada2_removeBimeraDenovo, dada2_seqCounts tabular, dada2_dada, dada2_errorrates, pdf, dada2_sequencetable, dada2_mergepairs, dada2_uniques DADA2 wrappers 2019-07-05 https://benjjneb.github.io/dada2/index.html 1.38.0 bioconductor-dada2 1.38.0 Up-to-date Metagenomics Variant calling, DNA barcoding Variant calling, DNA barcoding Sequencing, Genetic variation, Microbial ecology, Metagenomics Sequencing, Genetic variation, Microbial ecology, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dada2 dada2 dada2 This package infers exact sequence variants (SVs) from amplicon data, replacing the commonly used and coarser OTU clustering approach. This pipeline inputs demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier. microbiome/dada-16S 11 865 885 205808 209081 1301 1344 254475 270135 179 179 52639 52639 72 72 38131 38131 569986 551053 2480 2417 +das_tool Fasta_to_Contig2Bin, das_tool tabular, txt, fasta DAS Tool for genome resolved metagenomics 2022-06-23 https://github.com/cmks/DAS_Tool 1.1.7 das_tool 1.1.7 Up-to-date Metagenomics Read binning Read binning Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/das_tool /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/das_tool dastool dastool DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. 2 77 77 6906 6906 12 12 283 283 0 0 0 0 3 3 1185 1185 8374 8374 92 92 +dashing2 dashing2_dist, dashing2_sketch, dashing2_wsketch tabular, binary k-mer based tool for sketching and comparison of genomic sequences 2026-06-18 https://github.com/dnbaker/dashing2 2.1.20 dashing2 2.1.20 Up-to-date Sequence Analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dashing2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dashing2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +data_manager_homer_preparse homer_annotatePeaks, homer_findMotifs, homer_findMotifsGenome, homer_gtf_to_annotations, homer_scanMotifGenomeWide tabular, html, bed HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. 2021-08-08 http://homer.ucsd.edu/homer/index.html 4.11 homer 5.1 To update Sequence Analysis Sequence motif discovery Sequence motif discovery iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/homer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/homer homer homer HOMER contains a novel motif discovery algorithm that was designed for regulatory element analysis in genomics applications (DNA only, no protein). It is a differential motif discovery algorithm, which means that it takes two sets of sequences and tries to identify the regulatory elements that are specifically enriched in on set relative to the other. It uses ZOOPS scoring (zero or one occurrence per sequence) coupled with the hypergeometric enrichment calculations (or binomial) to determine motif enrichment. HOMER also tries its best to account for sequenced bias in the dataset. It was designed with ChIP-Seq and promoter analysis in mind, but can be applied to pretty much any nucleic acids motif finding problem. 5 293 293 11363 11363 0 0 0 0 0 0 0 0 23 24 388 534 11897 11751 317 316 +data_source_iris_tcga data_source_iris_tcga auto IRIS-TCGA Data source tool 2016-02-18 1.0.0 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/data_source_iris_tcga /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/data_source_iris_tcga 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +datamash datamash_ops, datamash_reverse, datamash_transpose GNU Datamash is a command-line program which performs basicnumeric,textual and statistical operations on input textual data files.It is designed to be portable and reliable, and aid researchersto easily automate analysis pipelines, without writing code or even short scripts.License: GPL Version 3 (or later).These tool wrappers were originally writen by Assaf Gordon. 2015-08-03 https://www.gnu.org/software/datamash/ 1.9 datamash 1.1.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/datamash /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/datamash https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://workflowhub.eu/workflows/403?version=9 microbiome/nanopore-16S-metagenomics 3 6000 6432 876492 892401 5184 5885 114632 134970 2485 2521 24641 25144 249 250 5920 5956 1058471 1021685 15088 13918 +decontam decontam png, tabular, phyloseq Removes decontamination features (ASVs/OTUs) using control samples 2024-09-13 https://github.com/benjjneb/decontam 1.22.0 bioconductor-decontam 1.30.0 To update Metagenomics Classification Classification Metagenomics, Microbial ecology, Sequencing Metagenomics, Microbial ecology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontam /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/decontam decontam decontam Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data. Requires DNA quantitation data or sequenced negative control samples. 1 8 8 32 32 0 0 0 0 0 0 0 0 0 0 0 0 32 32 8 8 +decontaminator decontaminator tabular, fasta Deep Learning method for novel virus detection in sequencing data 2023-01-09 https://github.com/cbib/decontaminator 1.0.0 numpy To update Machine Learning Filtering Filtering Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/decontaminator /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/decontaminator decontaminator decontaminator Decontaminator is a deep learning helping tool that filters out phage or fungi contigs from plant virome RNAseq assemblies. 1 41 41 349 349 0 0 0 0 0 0 0 0 0 0 0 0 349 349 41 41 +deeparg deeparg_predict, deeparg_short_reads tabular A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes 2024-10-07 https://github.com/gaarangoa/deeparg 1.0.4 deeparg 1.0.4 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Antimicrobial resistance prediction Antimicrobial resistance prediction, Antimicrobial resistance prediction Microbiology Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deeparg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deeparg deeparg DeepARG A deep learning based approach to predict Antibiotic Resistance Genes (ARGs) from metagenomes. 2 20 20 108 108 0 0 0 0 0 0 0 0 4 4 65 65 173 173 24 24 +deepmicro deepmicro tabular Representation learning and classification framework 2023-03-16 https://github.com/paulzierep/DeepMicro 1.4 deepmicro 1.4 Up-to-date Machine Learning Essential dynamics, Splitting, Community profiling Essential dynamics, Splitting Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics Microbial ecology, Machine learning, Pathology, Public health and epidemiology, Allergy, clinical immunology and immunotherapeutics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepmicro /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deepmicro DeepMicro DeepMicro Deep representation learning for disease prediction based on microbiome data.DeepMicro is a deep representation learning framework exploiting various autoencoders to learn robust low-dimensional representations from high-dimensional data and training classification models based on the learned representation. 1 9 9 560 560 0 0 0 0 0 0 0 0 0 0 0 0 560 560 9 9 +deepsig deepsig gff3 Predictor of signal peptides in proteins based on deep learning 2023-04-28 https://github.com/BolognaBiocomp/deepsig 1.2.5 deepsig 1.2.5 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepsig /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deepsig https://usegalaxy.eu/published/workflow?id=a018307be3563f28 1 131 131 388 388 0 0 0 0 0 0 0 0 11 11 45 45 433 433 142 142 +deepvariant deepvariant vcf, html DeepVariant is a deep learning-based variant caller 2021-09-06 https://github.com/google/deepvariant 1.10.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deepvariant 1 546 546 5121 5121 789 789 6696 6696 0 0 0 0 0 0 0 0 11817 11817 1335 1335 +deg_annotate deg_annotate tabular Annotate DESeq2/DEXSeq output tables 2018-11-22 https://github.com/galaxyproject/tools-iuc/tree/master/tools/deg_annotate 1.1.0 bedtools 2.31.1 To update Transcriptomics, Single Cell RNA-Seq analysis, Gene functional annotation RNA-Seq analysis, Gene functional annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deg_annotate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deg_annotate deg_annotate DEG Annotate This tool appends the output table of DESeq2 or DEXSeq with gene symbols, biotypes, positions etc. The information you want to add is configurable. This information should present in the input GTF/GFF file as attributes of feature you choose. https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1 1 5016 5484 28041 30372 6635 6880 40314 41985 1207 1251 6149 6366 185 186 649 665 79388 75153 13801 13043 +delly delly_call, delly_classify, delly_cnv, delly_filter, delly_lr, delly_merge bcf, tabular.gz Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends, split-reads and read-depth to sensitively and accurately delineate genomic rearrangements throughout the genome. 2020-09-28 https://github.com/dellytools/delly 0.9.1 delly 2.1.0 To update Variant Analysis Indel detection, Structural variation detection, Variant calling, Genotyping, Genetic variation analysis Indel detection, Structural variation detection, Genotyping DNA structural variation, Sequencing, Pathology, Genomics, Genetic variation, Bioinformatics, Population genomics, Rare diseases Sequencing, Genetic variation, Bioinformatics, Population genomics, Rare diseases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/delly /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/delly delly2 Delly2 Integrated structural variant prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout the genome. Structural variants can be visualized using Delly-maze and Delly-suave. 6 185 185 3117 3117 0 0 0 0 0 0 0 0 0 0 0 0 3117 3117 185 185 +deseq2 deseq2 tabular, pdf Differential gene expression analysis based on the negative binomial distribution 2014-12-03 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html 2.11.40.8 bioconductor-deseq2 1.50.2 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis, RNA-Seq analysis Differential gene expression analysis, RNA-Seq analysis RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/deseq2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/deseq2 DESeq2 DESeq2 R/Bioconductor package for differential gene expression analysis based on the negative binomial distribution. Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1 1 13707 15994 110682 133936 27214 37996 191581 286575 2980 3614 19899 24448 820 824 4511 4530 449489 326673 58428 44721 +detect_circular_sequences detect_circular_sequences fasta, txt Detect circular sequences (e.g. circular contigs) in a FASTA file 2025-09-22 https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Sequence Analysis, Assembly https://github.com/galaxyproject/tools-iuc/tree/main/tools/detect_circular_sequences /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/detect_circular_sequences 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +dexseq dexseq, dexseq_count, plotdexseq tabular, html, rds, gtf, pdf Inference of differential exon usage in RNA-Seq 2015-09-25 https://www.bioconductor.org/packages/release/bioc/html/DEXSeq.html 1.48.0 bioconductor-dexseq 1.56.0 To update Transcriptomics, RNA, Statistics, Single Cell Enrichment analysis, Exonic splicing enhancer prediction Enrichment analysis, Exonic splicing enhancer prediction RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dexseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dexseq dexseq DEXSeq The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results. 3 274 481 14442 18733 646 1620 16356 30696 65 101 2756 4812 8 9 97 98 54339 33651 2211 993 +diamond bg_diamond, bg_diamond_makedb, bg_diamond_view txt, dmnd DIAMOND is a new alignment tool for aligning short DNA sequencing reads to a protein reference database such as NCBI-NR. 2021-03-21 https://github.com/bbuchfink/diamond 2.2.2 diamond 2.2.2 Up-to-date Sequence Analysis Sequence alignment analysis Sequence alignment analysis Sequence analysis, Proteins Sequence analysis, Proteins bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/diamond /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/diamond diamond Diamond Sequence aligner for protein and translated DNA searches and functions as a drop-in replacement for the NCBI BLAST software tools. It is suitable for protein-protein search as well as DNA-protein search on short reads and longer sequences including contigs and assemblies, providing a speedup of BLAST ranging up to x20,000. https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 3 1620 1706 112648 114376 665 1048 35921 43599 446 448 65850 66062 125 125 2180 2208 226245 216599 3327 2856 +diffbind diffbind interval, pdf, tabular, rdata, txt Diffbind provides functions for processing ChIP-Seq data. 2018-01-22 http://bioconductor.org/packages/release/bioc/html/DiffBind.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-diffbind 3.20.0 To update ChIP-seq Differential binding analysis Differential binding analysis ChIP-seq ChIP-seq bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffbind /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/diffbind diffbind DiffBind Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. 1 667 792 9452 11112 1268 2073 13935 20417 80 101 1868 2386 69 69 130 130 34045 25385 3035 2084 +diffdock diffdock Diffusion Steps, Twists, and Turns for Molecular Docking. 2025-06-27 https://github.com/gcorso/DiffDock 1.1.3 To update Computational chemistry iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/diffdock /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/diffdock 1 6 6 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 6 6 +dimet dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@, dimet_@EXECUTABLE@ DIMet is a bioinformatics pipeline for differential analysis of isotopic targeted labeling data. 2023-07-19 https://github.com/cbib/DIMet 0.2.4 dimet 0.2.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dimet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dimet 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +disco disco txt, fasta DISCO is a overlap-layout-consensus (OLC) metagenome assembler 2017-10-26 http://disco.omicsbio.org/ @WRAPPER_VERSION@.1 disco 1.3 To update Metagenomics, Assembly Protein sequence analysis Protein sequence analysis Structure determination Structure determination iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/disco /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/disco disco DISCO DISCO is software to perform structure determination of protein homo-oligomers with cyclic symmetry.DISCO computes oligomeric protein structures using geometric constraints derived from RDCs and intermolecular distance restraints such as NOEs or disulfide bonds. When a reliable subunit structure can be calculated from intramolecular restraints, DISCO guarantees that all satisfying oligomer structures will be discovered, yet can run in minutes to hours on only a single desktop-class computer. 1 127 163 280 453 406 435 1525 1690 0 0 0 0 0 0 0 0 2143 1805 598 533 +dnabot dnabot tar DNA assembly using BASIC on OpenTrons 2022-04-17 https://github.com/BASIC-DNA-ASSEMBLY/DNA-BOT @TOOL_VERSION@ dnabot To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnabot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dnabot 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +dnaweaver dnaweaver xlsx Given a SBOL input, calculate assembly parts for Gibson or Golden Gate. 2022-12-08 https://github.com/Edinburgh-Genome-Foundry/DnaWeaver @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ dnaweaver_synbiocad 1.0.2 To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dnaweaver /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dnaweaver 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +dos2unix dos2unix txt dos2unix convert text files with DOS or Mac line breaks to Unix line breaks and vice versa. 2025-07-11 https://waterlan.home.xs4all.nl/dos2unix.html 7.5.5 dos2unix To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dos2unix /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dos2unix 1 7 7 18 18 0 0 0 0 0 0 0 0 0 0 0 0 18 18 7 7 +dram dram_annotate, dram_distill, dram_merge_annotations, dram_neighborhoods, dram_strainer fasta, gff3, tabular, genbank, xlsx, html DRAM for distilling microbial metabolism to automate the curation of microbiome function 2022-09-01 https://github.com/WrightonLabCSU/DRAM 1.5.0 dram 1.5.0 Up-to-date Metagenomics Gene functional annotation Gene functional annotation Metagenomics, Biological databases, Molecular genetics Metagenomics, Biological databases, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dram /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dram dram DRAM Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes 5 120 120 13633 13633 0 0 0 0 0 0 0 0 0 0 0 0 13633 13633 120 120 +drep drep_compare, drep_dereplicate dRep compares and dereplicates genome sets 2020-01-06 https://github.com/MrOlm/drep 3.6.2 drep 3.6.2 Up-to-date Metagenomics Genome comparison Genome comparison Metagenomics, Genomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/drep drep dRep Fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. 2 113 115 1708 1749 13 13 47 47 0 0 0 0 38 38 1273 1273 3069 3028 166 164 +drhip drhip tabular Data Reduction for HyPhy with Inference Processing. A toolkit for analyzing and summarizing HyPhy evolutionary selection analysis results 2025-11-26 https://github.com/veg/DRHIP @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ drhip 0.1.5 To update Phylogenetics, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/drhip /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/drhip 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +dropletutils dropletutils tsv, h5, mtx, png DropletUtils - Utilities for handling droplet-based single-cell RNA-seq data 2019-06-04 https://bioconductor.org/packages/devel/bioc/html/DropletUtils.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-dropletutils 1.30.0 To update Single Cell, Sequence Analysis Loading, Community profiling Gene expression, RNA-seq, Sequencing, Transcriptomics Sequencing, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/dropletutils /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/dropletutils dropletutils DropletUtils Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix. 1 450 517 4128 4902 381 385 5328 5345 42 46 2038 2190 34 34 110 110 12547 11604 982 907 +drug2cell drug2cell h5ad Collection of utility functions for gene group activity evaluation in scanpy. 2025-01-21 https://github.com/Teichlab/drug2cell @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ drug2cell 0.1.2 To update Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/drug2cell /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/drug2cell 1 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 +duplex_family_size_distribution fsd, fsd_beforevsafter, fsd_regions, td pdf, tabular Tool that plots a histogram of sizes of read families 2019-10-24 1.0.2 matplotlib To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fsd /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fsd 4 0 0 0 0 12 13 326 612 0 0 0 0 0 0 0 0 612 326 13 12 +ebi_tools ebi_search_rest_results tabular Tools to query and download data from several EMBL-EBI databases 2016-11-29 http://www.ebi.ac.uk/services/all 0.1.1 six To update Web Services, Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ebi_tools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ebi_tools 1 121 180 187 431 449 587 1055 1533 0 0 0 0 1 1 1 1 1965 1243 768 571 +edger edger html, txt Perform RNA-Seq differential expression analysis using edgeR pipeline 2017-09-11 http://bioconductor.org/packages/release/bioc/html/edgeR.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-edger 4.8.2 To update Transcriptomics, RNA, Statistics, Single Cell Differential gene expression analysis Differential gene expression analysis Genetics, RNA-Seq, ChIP-seq Genetics, RNA-Seq, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/edger /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/edger edger edgeR Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, SAGE and CAGE. https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809 1 2767 3276 20681 25641 6109 8376 43822 64826 928 1075 7956 10252 29 30 172 173 100892 72631 12757 9833 +ega_download_client pyega3 txt, tabular EGA python client uses the EGA REST API to download authorized datasets and files. 2020-09-02 https://github.com/EGA-archive/ega-download-client @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ pyega3 5.2.0 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pyega3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pyega3 1 138 138 2852 2852 55 55 208 208 5 5 459 459 0 0 0 0 3519 3519 198 198 +egsea egsea html, txt, rdata This tool implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing 2017-12-28 https://bioconductor.org/packages/release/bioc/html/EGSEA.html 1.20.0 bioconductor-egsea 1.38.0 To update Transcriptomics, RNA, Statistics, Single Cell Gene set testing Gene set testing Systems biology Systems biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/egsea /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/egsea egsea EGSEA This package implements the Ensemble of Gene Set Enrichment Analyses method for gene set testing. 1 365 467 2481 3462 783 865 5041 5849 259 282 2025 2377 0 0 0 0 11688 9547 1614 1407 +emboss emboss_needle, emboss_needleall needle Galaxy wrappers for EMBOSS6 tools 2025-01-17 http://emboss.open-bio.org/ 6.6.0 emboss 6.6.0 Up-to-date Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/emboss emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 2 62 62 419 419 0 0 0 0 0 0 0 0 0 0 0 0 419 419 62 62 +emboss_5 EMBOSS: antigenic1, EMBOSS: backtranseq2, EMBOSS: banana3, EMBOSS: biosed4, EMBOSS: btwisted5, EMBOSS: cai6, EMBOSS: cai_custom6, EMBOSS: chaos7, EMBOSS: charge8, EMBOSS: checktrans9, EMBOSS: chips10, EMBOSS: cirdna11, EMBOSS: codcmp12, EMBOSS: coderet13, EMBOSS: compseq14, EMBOSS: cpgplot15, EMBOSS: cpgreport16, EMBOSS: cusp17, EMBOSS: cutseq18, EMBOSS: dan19, EMBOSS: degapseq20, EMBOSS: descseq21, EMBOSS: diffseq22, EMBOSS: digest23, EMBOSS: dotmatcher24, EMBOSS: dotpath25, EMBOSS: dottup26, EMBOSS: dreg27, EMBOSS: einverted28, EMBOSS: epestfind29, EMBOSS: equicktandem31, EMBOSS: est2genome32, EMBOSS: etandem33, EMBOSS: extractfeat34, EMBOSS: extractseq35, EMBOSS: freak36, EMBOSS: fuzznuc37, EMBOSS: fuzzpro38, EMBOSS: fuzztran39, EMBOSS: garnier40, EMBOSS: geecee41, EMBOSS: getorf42, EMBOSS: helixturnhelix43, EMBOSS: hmoment44, EMBOSS: iep45, EMBOSS: infoseq46, EMBOSS: isochore47, EMBOSS: lindna48, EMBOSS: marscan49, EMBOSS: maskfeat50, EMBOSS: maskseq51, EMBOSS: matcher52, EMBOSS: megamerger53, EMBOSS: merger54, EMBOSS: msbar55, EMBOSS: needle56, EMBOSS: newcpgreport57, EMBOSS: newcpgseek58, EMBOSS: newseq59, EMBOSS: noreturn60, EMBOSS: notseq61, EMBOSS: nthseq62, EMBOSS: octanol63, EMBOSS: oddcomp64, EMBOSS: palindrome65, EMBOSS: pasteseq66, EMBOSS: patmatdb67, EMBOSS: pepcoil68, EMBOSS: pepinfo69, EMBOSS: pepnet70, EMBOSS: pepstats71, EMBOSS: pepwheel72, EMBOSS: pepwindow73, EMBOSS: pepwindowall74, EMBOSS: plotcon75, EMBOSS: plotorf76, EMBOSS: polydot77, EMBOSS: preg78, EMBOSS: prettyplot79, EMBOSS: prettyseq80, EMBOSS: primersearch81, EMBOSS: revseq82, EMBOSS: seqmatchall83, EMBOSS: seqret84, EMBOSS: showfeat85, EMBOSS: shuffleseq87, EMBOSS: sigcleave88, EMBOSS: sirna89, EMBOSS: sixpack90, EMBOSS: skipseq91, EMBOSS: splitter92, EMBOSS: supermatcher95, EMBOSS: syco96, EMBOSS: tcode97, EMBOSS: textsearch98, EMBOSS: tmap99, EMBOSS: tranalign100, EMBOSS: transeq101, EMBOSS: trimest102, EMBOSS: trimseq103, EMBOSS: twofeat104, EMBOSS: union105, EMBOSS: vectorstrip106, EMBOSS: water107, EMBOSS: wobble108, EMBOSS: wordcount109, EMBOSS: wordmatch110 antigenic, txt, btwisted, cai, png, charge, checktrans, fasta, gff, chips, codcmp, coderet, compseq, cpgplot, cpgreport, cusp, dan, diffseq, digest, dreg, einverted, epestfind, table, equicktandem, est2genome, etandem, freak, fuzznuc, fuzzpro, fuzztran, garnier, geecee, motif, hmoment, isochore, markx0, simple, needle, newcpgreport, newcpgseek, noreturn, oddcomp, palindrome, dbmotif, pepcoil, pepinfo, pepstats, polydot, preg, prettyseq, primersearch, seqmatchall, showfeat, sixpack, supermatcher, syco, textsearch, seqtable, vectorstrip, srs, wobble, wordcount, match Galaxy wrappers for EMBOSS version 5.0.0 tools 2017-01-11 http://emboss.open-bio.org/ 5.0.0 emboss 6.6.0 To update Sequence Analysis, Fasta Manipulation Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Sequence analysis, Local alignment, Sequence alignment analysis, Global alignment, Sequence alignment Molecular biology, Sequence analysis, Biology Molecular biology, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/emboss_5 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/emboss_5 emboss EMBOSS Diverse suite of tools for sequence analysis; many programs analagous to GCG; context-sensitive help for each tool. 107 444 513 264479 273772 1350 2518 169846 325994 557 810 29757 35329 51 51 997 1037 636132 465079 3892 2402 +ena_upload ena_upload txt, tabular Submits experimental data and respective metadata to the European Nucleotide Archive (ENA). 2020-06-10 https://github.com/usegalaxy-eu/ena-upload-cli @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ena-upload-cli 0.10.1 To update Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_upload /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ena_upload 1 48 48 418 418 0 0 0 0 15 15 1833 1833 0 0 0 0 2251 2251 63 63 +ena_webin_cli ena_webin_cli txt, tar Submits a genome assembly to the European Nucleotide Archive (ENA) using the Webin-CLI Submission tool. 2025-02-27 https://ena-docs.readthedocs.io/en/latest/submit/general-guide/webin-cli.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ena-webin-cli 9.0.3 To update Data Export iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ena_webin_cli /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ena_webin_cli 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +enasearch enasearch_retrieve_analysis_report, enasearch_retrieve_data, enasearch_retrieve_run_report, enasearch_retrieve_taxons, enasearch_search_data tabular A Python library for interacting with ENA's API 2017-08-05 https://github.com/bebatut/enasearch @WRAPPER_VERSION@.0 enasearch 0.2.2 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/enasearch /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/enasearch 5 161 221 1661 2454 0 0 0 0 0 0 0 0 0 0 0 0 2454 1661 221 161 +endorspy endorspy json Calculate endogenous DNA percentage, clonality, and duplicates from samtools flagstats. 2026-03-10 https://github.com/aidaanva/endorS.py @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/endorspy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/endorspy 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ensembl_vep ensembl_vep vcf, txt Ensembl VEP: Annotate VCFs with variant effect predictions 2022-05-11 https://github.com/Ensembl/ensembl-vep @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ensembl-vep 116.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ensembl_vep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ensembl_vep 1 269 269 3860 3860 0 0 0 0 0 0 0 0 0 0 0 0 3860 3860 269 269 +episcanpy episcanpy_build_matrix, episcanpy_cluster_embed, episcanpy_preprocess h5ad, txt, png EpiScanpy – Epigenomics single cell analysis in python 2023-03-13 https://github.com/colomemaria/epiScanpy 0.3.2 episcanpy 0.4.0 To update Single Cell, Epigenetics Enrichment analysis, Imputation Enrichment analysis, Imputation Epigenomics, Cell biology, DNA Epigenomics, Cell biology, DNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/episcanpy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/episcanpy episcanpy epiScanpy Epigenomics Single Cell Analysis in Python. 0 53 53 1075 1075 53 53 406 406 2 2 766 766 0 0 0 0 2247 2247 108 108 +ete_treeviewer ete_treeviewer svg A toolkit for the analysis and visualization of trees. 2024-11-25 http://etetoolkit.org @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ curl To update Phylogenetics Phylogenetic analysis, Phylogenetic tree editing Phylogenetic tree editing Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ete-toolkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ete-toolkit ete ete The Environment for Tree Exploration (ETE) is a computational framework that simplifies the reconstruction, analysis, and visualization of phylogenetic trees and multiple sequence alignments. Here, we present ETE v3, featuring numerous improvements in the underlying library of methods, and providing a novel set of standalone tools to perform common tasks in comparative genomics and phylogenetics. The new features include (i) building gene-based and supermatrix-based phylogenies using a single command, (ii) testing and visualizing evolutionary models, (iii) calculating distances between trees of different size or including duplications, and (iv) providing seamless integration with the NCBI taxonomy database. ETE is freely available at http://etetoolkit.org 1 130 130 1626 1626 0 0 0 0 0 0 0 0 4 4 5 5 1631 1631 134 134 +eukrep eukrep fasta, txt Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 2025-07-30 https://github.com/patrickwest/EukRep @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ eukrep 0.6.7 To update Metagenomics Nucleic acid sequence analysis Nucleic acid sequence analysis Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/eukrep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/eukrep eukrep EukRep Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +evidencemodeler evidencemodeler gff, fasta EVidenceModeler (EVM) combines ab intio genetic predictions with protein and transcript alignments in weighted consensus genetic structures. 2024-07-19 https://github.com/EVidenceModeler/EVidenceModeler?tab=readme-ov-file 2.1.0 evidencemodeler 2.1.0 Up-to-date Genome annotation Gene prediction Gene prediction Gene expression, Gene structure Gene expression, Gene structure iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/evidencemodeler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/evidencemodeler EvidenceModeler EvidenceModeler The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system. 1 12 12 27 27 0 0 0 0 0 0 0 0 0 0 0 0 27 27 12 12 +exomedepth exomedepth tabular ExomeDepth: Calls copy number variants (CNVs) from targeted sequence data 2019-11-08 https://cran.r-project.org/package=ExomeDepth 1.1.0 r-exomedepth 1.1.18 To update Sequence Analysis, Variant Analysis Sequence analysis, Variant calling, Genotyping, Copy number estimation Sequence analysis, Variant calling, Genotyping, Copy number estimation Exome sequencing, Gene transcripts, Mapping, Sequencing, Genetic variation, Rare diseases Exome sequencing, Gene transcripts, Mapping, Genetic variation, Rare diseases crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/exomedepth /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/exomedepth exomedepth ExomeDepth Copy number variant (CNV) calling algorithm designed to control technical variability between samples. It calls CNVs from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. 1 61 72 540 607 183 203 2916 3164 0 0 0 0 0 0 0 0 3771 3456 275 244 +exonerate exonerate gff, gff3, txt Exonerate is a generic tool for pairwise sequence comparison. 2018-08-02 https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate 2.4.0 exonerate 2.4.0 Up-to-date Sequence Analysis Pairwise sequence alignment, Protein threading, Genome alignment Pairwise sequence alignment, Protein threading, Genome alignment Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks Sequence analysis, Sequence sites, features and motifs, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/exonerate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/exonerate exonerate Exonerate A tool for pairwise sequence alignment. It enables alignment for DNA-DNA and DNA-protein pairs and also gapped and ungapped alignment. 1 184 212 829 1242 191 222 733 1220 39 39 1230 1230 26 27 570 582 4274 3362 500 440 +export2graphlan export2graphlan txt export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn 2017-03-03 https://bitbucket.org/CibioCM/export2graphlan/overview @VERSION@+@GALAXY_VERSION@ export2graphlan 0.22 To update Metagenomics Conversion Conversion Taxonomy, Metabolomics, Biomarkers Taxonomy, Metabolomics, Biomarkers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/export2graphlan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/export2graphlan export2graphlan export2graphlan export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn. In particular, the annotation file tries to highlight specific sub-trees deriving automatically from input file what nodes are important. https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 1 589 710 6276 7303 193 213 712 791 122 123 616 632 16 16 43 43 8769 7647 1062 920 +extract_genomic_dna Extract genomic DNA 1 Contains a tool that extracts genomic DNA using coordinates from ASSEMBLED genomes and UNassembled genomes. 2016-01-14 3.0.3 bx-python 0.14.0 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/extract_genomic_dna /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/extract_genomic_dna 1 930 1169 9749 15264 1876 12291 18355 263352 0 63 0 611 0 3 0 201 279428 28104 13526 2806 +fairy fairy_cov, fairy_sketch tabular, bcsp Fast approximate contig coverage for metagenomic binning 2024-12-20 https://github.com/bluenote-1577/fairy 0.5.8 fairy 0.5.8 Up-to-date Metagenomics Read binning, Sequence assembly validation Read binning, Sequence assembly validation Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fairy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fairy fairy fairy fast approximate contig coverage for metagenomic binningFairy computes multi-sample contig coverage for metagenome-assembled genome (MAG) binning.Fairy is used after metagenomic assembly and before binning. It can- Calculate coverage 100x-1000x faster than read alignment (e.g. BWA)- Give comparable bins for multi-sample binning (short read or nanopore reads)- Output formats that are compatible with MetaBAT2, MaxBin2, SemiBin2, and more 2 5 5 148 148 0 0 0 0 0 0 0 0 0 0 0 0 148 148 5 5 +falco falco html, txt A high throughput sequence QC analysis tool 2024-04-17 https://github.com/smithlabcode/falco/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ falco 1.3.2 To update Sequence Analysis Sequencing quality control, Visualisation, Read mapping Sequencing quality control, Visualisation, Read mapping Workflows, Mapping, Imaging Workflows, Mapping, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/falco /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/falco falco Falco A high-speed FastQC emulation for quality control of sequencing data. 1 3878 3878 162045 162045 965 965 16492 16492 274 274 5029 5029 24 24 357 357 183923 183923 5141 5141 +fargene fargene txt, tar.gz fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) 2019-08-30 https://github.com/fannyhb/fargene 0.1 fargene 0.1 Up-to-date Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Public health and epidemiology, Antimicrobial resistance Metagenomics, Microbiology, Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fargene /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fargene fargene fARGene fARGene (Fragmented Antibiotic Resistance Gene iENntifiEr ) is a tool that takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output. 1 150 159 895 1011 262 287 1203 1346 0 0 0 0 2 2 2 2 2359 2100 448 414 +fasta_clipping_histogram cshl_fasta_clipping_histogram png Length Distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_clipping_histogram /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fasta_clipping_histogram 1 45 45 306 306 0 0 0 0 96 140 5703 6332 1 1 1 1 6639 6010 186 142 +fasta_formatter cshl_fasta_formatter fasta FASTA Width formatter 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_formatter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fasta_formatter https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c 1 363 452 12086 12696 479 2140 4061 26449 76 107 733 1260 8 9 50 60 40465 16930 2708 926 +fasta_nucleotide_changer cshl_fasta_nucleotides_changer RNA/DNA converter. 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fasta_nucleotide_changer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fasta_nucleotide_changer 1 74 125 383 882 207 747 1415 5767 18 24 427 550 6 8 20 31 7230 2245 904 305 +fasta_nucleotide_color_plot fasta_nucleotide_color_plot png Contains a tool that produces a graphical representation of FASTA data with each nucleotide represented by a selected color. 2016-03-06 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/fourcolorplot 1.0.1 openjdk To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_nucleotide_color_plot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fasta_nucleotide_color_plot 1 55 65 392 494 170 230 745 1074 0 0 0 0 0 0 0 0 1568 1137 295 225 +fasta_stats fasta-stats tabular, bed Display summary statistics for a fasta file. 2018-11-21 https://github.com/galaxyproject/tools-iuc/tree/master/tools/fasta_stats/ 2.0 numpy To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasta_stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fasta_stats https://workflowhub.eu/workflows/403?version=9 1 3829 4225 56351 58340 4298 4623 34345 35598 2435 3021 17734 22805 147 147 749 749 117492 109179 12016 10709 +fastani fastani tabular Fast alignment-free computation of whole-genome Average Nucleotide Identity 2020-02-17 https://github.com/ParBLiSS/FastANI 1.3 fastani 1.34 To update Sequence Analysis Genome alignment, Sequence similarity search Genome alignment, Sequence similarity search Microbiology, Genetic variation Microbiology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastani /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastani fastani FastANI FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. 1 1182 1205 29436 29626 1 1 18 18 133 133 1799 1799 64 64 949 949 32392 32202 1403 1380 +fastga alnchain, fastga binary, paf Galaxy wrapper for FastGA 2026-02-20 https://github.com/thegenemyers/FASTGA 1.5 fastga 1.5 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastga /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastga 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fastk fastk_fastk, fastk_histex, fastk_logex fastk_ktab_tar, fastk_hist, fastk_ktab, txt, tabular FastK: A K-mer counter (for HQ assembly data sets) 2024-05-03 https://github.com/thegenemyers/FASTK 1.1.0 fastk 1.2 To update Assembly k-mer counting, Sequence analysis k-mer counting, Sequence analysis Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastk fastk FASTK FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. 3 46 46 742 742 45 45 389 389 0 0 0 0 0 0 0 0 1131 1131 91 91 +fastoma fastoma xml, html, ipynb, tabular, newick FastOMA is a scalable tool for orthology inference among many genomes. 2025-12-26 https://github.com/dessimozlab/FastOMA 0.5.1 To update Phylogenetics, Sequence Analysis Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) Phylogenetic tree reconciliation, Protein sequence analysis, Genome comparison, Sequence clustering, Phylogenetic inference (from molecular sequences) Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastoma /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastoma fastoma FastOMA FastOMA is a scalable software package to infer orthology relationship. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fastp fastp html, json Fast all-in-one preprocessing for FASTQ files 2018-03-08 https://github.com/OpenGene/fastp 1.3.5 fastp 1.3.5 Up-to-date Sequence Analysis Sequencing quality control, Sequence contamination filtering Sequence contamination filtering Sequence analysis, Probes and primers Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastp fastp fastp A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 10510 10845 1229203 1372687 13972 14837 495065 537410 3030 3115 99990 109532 303 306 30703 30747 2050376 1854961 29103 27815 +fastplong fastplong html, json, fastq Fastplong is used for ultrafast preprocessing and quality control for long reads (Nanopore, PacBio, Cyclone, etc.). 2025-05-06 https://github.com/OpenGene/fastplong @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ fastplong 0.4.1 To update Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastplong /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastplong 1 40 40 309 309 0 0 0 0 8 8 217 217 0 0 0 0 526 526 48 48 +fastq_combiner fastq_combiner fastqsanger Combine FASTA and QUAL into FASTQ 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_combiner /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_combiner 1 241 306 9199 9921 880 3131 50082 77184 83 102 1967 2373 16 17 353 354 89832 61601 3556 1220 +fastq_dl fastq_dl Download FASTQ files from ENA. 2024-11-14 https://github.com/rpetit3/fastq-dl 4.0.1 fastq-dl 4.0.1 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_dl /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastq_dl https://usegalaxy.eu/published/workflow?id=02f90a96d01fed4f 1 62 62 303 303 167 167 621 621 0 0 0 0 0 0 0 0 924 924 229 229 +fastq_filter fastq_filter Filter FASTQ reads by quality score and length 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_filter https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c 1 867 1046 22450 29161 2532 9682 35516 127334 219 331 4753 6800 84 84 436 436 163731 63155 11143 3702 +fastq_groomer fastq_groomer fastqsanger Convert between various FASTQ quality formats. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_groomer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_groomer 1 3066 3798 107854 130022 8079 45933 145592 914641 656 1191 15303 28714 206 208 7929 8019 1081396 276678 51130 12007 +fastq_groupmerge fastq_groupmerge A tool for merging fastq reads by metadata 2025-11-09 https://github.com/SantaMcCloud/fastq-groupmerge @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ fastq-groupmerge 1.0.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastq_groupmerge /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastq_groupmerge 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fastq_manipulation fastq_manipulation Manipulate FASTQ reads on various attributes. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_manipulation /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_manipulation 1 180 285 5124 6437 622 2173 5410 15997 86 164 3990 5357 15 15 503 503 28294 15027 2637 903 +fastq_masker_by_quality fastq_masker_by_quality FASTQ Masker by quality score 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_masker_by_quality 1 58 61 675 733 244 1008 2111 8416 13 21 398 577 8 8 34 34 9760 3218 1098 323 +fastq_paired_end_deinterlacer fastq_paired_end_deinterlacer FASTQ de-interlacer on paired end reads. 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_paired_end_deinterlacer 1 561 775 8915 13227 1973 2832 14532 22941 202 284 2045 3031 57 57 730 730 39929 26222 3948 2793 +fastq_paired_end_interlacer fastq_paired_end_interlacer FASTQ interlacer on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_paired_end_interlacer https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 1 2968 3318 27989 31403 4447 5152 25343 30506 1649 1748 7253 8107 135 135 1103 1103 71119 61688 10353 9199 +fastq_paired_end_joiner fastq_paired_end_joiner FASTQ joiner on paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_paired_end_joiner 1 570 793 12982 18847 1661 5991 21263 61308 152 243 1664 2619 25 25 236 236 83010 36145 7052 2408 +fastq_paired_end_splitter fastq_paired_end_splitter FASTQ splitter on joined paired end reads 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_paired_end_splitter 1 515 636 4433 4974 1317 3616 27563 40409 209 281 865 1229 17 17 45 45 46657 32906 4550 2058 +fastq_quality_boxplot cshl_fastq_quality_boxplot png Draw quality score boxplot 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_boxplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastq_quality_boxplot 1 126 192 1189 1420 2021 9265 12840 61870 36 63 207 541 13 13 89 90 63921 14325 9533 2196 +fastq_quality_converter cshl_fastq_quality_converter fastq Quality format converter (ASCII-Numeric) 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_converter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastq_quality_converter 1 48 58 279 380 216 2253 1115 9736 14 30 1232 1623 4 4 21 21 11760 2647 2345 282 +fastq_quality_filter cshl_fastq_quality_filter Filter by quality 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_quality_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastq_quality_filter 1 4665 5314 37994 40749 6202 14016 45014 145519 1994 2474 8377 11391 335 340 1344 1394 199053 92729 22144 13196 +fastq_stats fastq_stats tabular FASTQ Summary Statistics by column 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_stats 1 678 941 3662 5208 2614 14639 13510 84786 161 293 3484 4398 53 53 296 296 94688 20952 15926 3506 +fastq_to_fasta cshl_fastq_to_fasta fasta, fasta.gz FASTQ to FASTA converter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastq_to_fasta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastq_to_fasta 1 2014 2152 50989 55713 3019 7213 46867 109930 530 837 10769 18067 211 211 3227 3227 186937 111852 10413 5774 +fastq_to_tabular fastq_to_tabular tabular FASTQ to Tabular converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_to_tabular /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_to_tabular https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 1 314 388 13805 20661 637 1959 14158 34744 78 113 6297 7058 27 27 2036 2036 64499 36296 2487 1056 +fastq_trimmer fastq_trimmer FASTQ Trimmer by quality 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastq_trimmer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastq_trimmer 1 603 788 10307 12822 1895 9246 22836 96214 118 245 2064 3428 16 16 156 156 112620 35363 10295 2632 +fastqc fastqc html, txt Read QC reports using FastQC 2017-01-11 http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ 0.74 fastqc 0.12.1 To update Fastq Manipulation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequence composition calculation, Sequencing quality control, Statistical calculation Sequencing, Data quality management, Sequence analysis Sequencing, Data quality management, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastqc fastqc FastQC This tool aims to provide a QC report which can spot problems or biases which originate either in the sequencer or in the starting library material. It can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files. https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792, https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=8edf456f4aeddaac, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 microbiome/beer-data-analysis, microbiome/metagenomics-assembly, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 51266 57567 2264162 2546070 101879 164033 2763731 4007928 16002 19516 485637 571728 4458 4469 201980 202663 7328389 5715510 245585 173605 +fastqe fastqe html FASTQE 2020-07-13 https://fastqe.com/ 0.3.1 fastqe 0.5.2 To update Sequence Analysis Sequencing quality control Sequencing quality control Sequence analysis, Sequencing Sequence analysis, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastqe /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastqe fastqe FASTQE Compute quality stats for FASTQ files and print those stats as emoji... for some reason. 1 3154 3177 6904 6978 6143 6198 13534 13627 1316 1323 3505 3549 291 291 510 510 24664 24453 10989 10904 +fastqtofasta fastq_to_fasta_python fasta FASTQ to FASTA converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/fastqtofasta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/fastqtofasta https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://workflowhub.eu/workflows/403?version=9 1 3845 4522 249408 274687 5714 14677 147702 280466 876 876 22007 22007 3 3 3 3 577163 419120 20078 10438 +fastreer fastreer_dist2tree, fastreer_fasta2dist, fastreer_vcf2dist, fastreer_vcf2tree newick, txt fastreeR toolkit wrappers for phylogenetic trees and distance matrices from VCF and FASTA 2025-11-01 https://github.com/gkanogiannis/fastreeR 2.2.0 fastreer 2.2.0 Up-to-date Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastreer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastreer fastreer 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fastspar fastspar, fastspar_pvalues, fastspar_reduce tabular Tool for rapid and scalable correlation estimation for compositional data. 2025-06-16 https://github.com/scwatts/fastspar/ 1.0.0 fastspar 1.0.0 Up-to-date Metagenomics, Statistics Metagenomics, Microbial ecology Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fastspar /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fastspar FastSpar FastSpar FastSpar is a C++ implementation of the SparCC algorithm for fast correlation estimation from compositional count data such as microbiome OTU tables. 3 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 +fasttree fasttree nhx, txt FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences - GVL 2018-02-02 http://www.microbesonline.org/fasttree/ @VERSION@ fasttree 2.2.0 To update Phylogenetics Phylogenetic tree generation (from molecular sequences), Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fasttree /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fasttree fasttree FastTree Infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1826 1923 84447 85175 2879 3069 29857 32881 829 967 8573 9437 82 84 411 416 127909 123288 6043 5616 +fastx_artifacts_filter cshl_fastx_artifacts_filter Remove sequencing artifacts 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_artifacts_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_artifacts_filter 1 73 114 1004 2340 265 2463 3432 26090 27 55 666 1270 3 3 4 4 29704 5106 2635 368 +fastx_barcode_splitter cshl_fastx_barcode_splitter tabular Barcode Splitter 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_barcode_splitter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_barcode_splitter 1 259 312 37602 40250 977 2966 52272 112642 57 80 868 1228 16 16 49 49 154169 90791 3374 1309 +fastx_clipper cshl_fastx_clipper Clip adapter sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_clipper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_clipper 1 236 294 3335 4086 1087 6193 14946 122932 41 65 478 882 6 6 27 27 127927 18786 6558 1370 +fastx_collapser cshl_fastx_collapser fasta Collapse sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_collapser /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_collapser 1 401 459 59500 89761 876 3332 82238 206527 71 97 23810 25032 43 44 223 233 321553 165771 3932 1391 +fastx_nucleotides_distribution cshl_fastx_nucleotides_distribution png Draw nucleotides distribution chart 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Graphics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_nucleotides_distribution /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_nucleotides_distribution 1 55 98 140 293 1246 4541 5121 26678 73 105 1083 1309 8 9 11 12 28292 6355 4753 1382 +fastx_quality_statistics cshl_fastx_quality_statistics txt Compute quality statistics 2018-04-24 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Statistics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_quality_statistics /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_quality_statistics 1 145 219 2175 2409 4427 11117 34705 77345 292 343 3332 3945 5 5 65 65 83764 40277 11684 4869 +fastx_renamer cshl_fastx_renamer Rename sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_renamer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_renamer 1 224 280 4631 5145 276 1075 9882 15505 54 75 498 834 13 13 632 632 22116 15643 1443 567 +fastx_reverse_complement cshl_fastx_reverse_complement Reverse-Complement 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fastq Manipulation, Fasta Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_reverse_complement /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_reverse_complement 1 456 552 11586 15931 593 1664 17732 70434 82 105 853 1100 22 22 3557 3557 91022 33728 2343 1153 +fastx_trimmer cshl_fastx_trimmer Trim sequences 2017-07-10 http://hannonlab.cshl.edu/fastx_toolkit/ 0.0.14 fastx_toolkit 0.0.14 Up-to-date Fasta Manipulation, Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fastx_toolkit/fastx_trimmer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fastx_toolkit/fastx_trimmer 1 658 834 14961 18093 1662 8605 113603 224353 223 293 3364 5948 257 258 1669 1672 250066 133597 9990 2800 +featurecounts featurecounts tabular, bam featureCounts counts the number of reads aligned to defined masked regions in a reference genome 2016-02-09 https://subread.sourceforge.net/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ subread 2.1.1 To update RNA, Transcriptomics, Sequence Analysis Read summarisation, RNA-Seq quantification Read summarisation, RNA-Seq quantification RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/featurecounts /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/featurecounts featurecounts FeatureCounts featureCounts is a very efficient read quantifier. It can be used to summarize RNA-seq reads and gDNA-seq reads to a variety of genomic features such as genes, exons, promoters, gene bodies and genomic bins. It is included in the Bioconductor Rsubread package and also in the SourceForge Subread package. https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f, https://usegalaxy.eu/published/workflow?id=63478edcea3f449a, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=deec04097a871646 1 14615 16504 807686 914668 26510 33788 760980 995817 2872 3227 79521 90365 1581 1583 52228 52279 2053129 1700415 55102 45578 +feelnc feelnc gtf, txt Galaxy wrapper for FEELnc 2018-03-27 https://github.com/tderrien/FEELnc @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ feelnc 0.2 To update Sequence Analysis Annotation, Classification Annotation, Classification RNA-seq, Functional, regulatory and non-coding RNA Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/feelnc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/feelnc feelnc FEELnc A tool to annotate long non-coding RNAs from RNA-seq assembled transcripts. 1 139 151 1531 1740 143 156 1171 1283 8 8 115 115 15 15 71 71 3209 2888 330 305 +fermikit fermi2, fermikit_variants fastqsanger.gz, vcf FermiKit is a de novo assembly based variant calling pipeline for deep Illumina resequencing data. 2017-01-05 https://github.com/lh3/fermikit @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ fermi2 r193 To update Assembly, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fermikit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fermikit 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fgbio fgbio_findswitchbackreads bam, pdf fgbio 2025-11-04 https://github.com/fulcrumgenomics/fgbio 2.1.0 fgbio 4.1.0 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/fgbio /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/fgbio 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fgsea fgsea tabular, pdf, rdata Perform gene set testing using fgsea 2018-10-20 https://bioconductor.org/packages/release/bioc/html/fgsea.html 1.8.0 bioconductor-fgsea 1.36.2 To update Visualization, Transcriptomics, Statistics, Single Cell Gene-set enrichment analysis Gene-set enrichment analysis Genetics Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fgsea /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fgsea fgsea fgsea The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction. https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383 1 632 734 7520 8942 1072 1156 22759 24664 121 136 1144 1277 9 9 115 115 34998 31538 2035 1834 +fileidentification fileidentification txt Tool to check multimedia files if they are corrupt or duplicated 2025-10-28 https://github.com/dasch-swiss/fileidentification 2.5.0 To update Data Source, Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fileidentification /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fileidentification 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +filtlong filtlong fastqsanger Filtlong - Filtering long reads by quality 2018-09-14 https://github.com/rrwick/Filtlong 0.3.1 filtlong 0.3.1 Up-to-date Fastq Manipulation, Sequence Analysis Filtering, Sequencing quality control Filtering, Sequencing quality control iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/filtlong /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/filtlong filtlong Filtlong Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. 1 2169 2318 79820 82849 1410 1424 72145 72255 830 830 17538 17538 27 27 150 150 172792 169653 4599 4436 +flair flair_collapse, flair_correct gtf, bed, fasta, bed12 FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. 2020-11-06 https://github.com/BrooksLabUCSC/flair 1.5 flair 3.0.0 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/flair /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/flair 2 29 29 2028 2028 0 0 0 0 0 0 0 0 0 0 0 0 2028 2028 29 29 +flash flash tabular, txt Fast Length Adjustment of SHort reads 2017-09-25 https://ccb.jhu.edu/software/FLASH/ @VERSION@.4 flash 1.2.11 To update Assembly, Fastq Manipulation Read pre-processing, Sequence merging, Sequence assembly Read pre-processing, Sequence merging, Sequence assembly Sequencing, Sequence assembly Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/flash /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/flash flash FLASH Identifies paired-end reads which overlap in the middle, converting them to single long reads 1 257 325 36629 39853 417 787 10871 18175 1 1 4 4 0 0 0 0 58032 47504 1113 675 +flavotyper flavotyper tabular In silico serotyping of Flavobacterium psychrophilum from genome assemblies 2026-06-12 https://forge.inrae.fr/eric.duchaud/flavotyper 0.5.1 flavotyper 0.5.1 Up-to-date Sequence Analysis Sequence similarity search Sequence similarity search Whole genome sequencing, Genotype and phenotype, Microbiology, Veterinary medicine Whole genome sequencing, Genotype and phenotype, Microbiology, Veterinary medicine iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/flavotyper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/flavotyper flavotyper FlavoTyper FlavoTyper is a bioinformatics tool that performs in silico serotyping of Flavobacterium psychrophilum genome assemblies. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +fraggenescan fraggenescan tabular, fasta, gff Tool for finding (fragmented) genes in short read 2017-09-04 https://sourceforge.net/projects/fraggenescan/ @WRAPPER_VERSION@.0 fraggenescan 1.32 To update Sequence Analysis Gene prediction Gene prediction Genetics, Sequence analysis Genetics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fraggenescan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fraggenescan fraggenescan FragGeneScan Application for finding (fragmented) genes in short reads 1 160 193 1267 1643 0 0 0 0 48 48 1171 1208 2 2 12 12 2863 2450 243 210 +freebayes freebayes, bamleftalign vcf, bed, txt, bam Galaxy Freebayes Bayesian genetic variant detector tool 2017-01-11 https://github.com/ekg/freebayes 1.3.10 freebayes 1.3.10 Up-to-date Variant Analysis Variant calling, Statistical calculation Variant calling, Statistical calculation Genomics, Genetic variation, Rare diseases Genomics, Genetic variation, Rare diseases devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/freebayes /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/freebayes freebayes FreeBayes Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, multi-nucleotide polymorphisms, and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment. 2 8440 9638 175340 204865 14740 26159 140150 287235 1921 2607 23952 29522 246 246 2943 2946 524568 342385 38650 25347 +freyja freyja_aggregate_plot, freyja_boot, freyja_demix, freyja_variants tabular, html, pdf, csv lineage abundances estimation 2022-07-05 https://github.com/andersen-lab/Freyja 2.0.1 freyja 2.0.3 To update Metagenomics, Sequence Analysis RNA-Seq quantification RNA-Seq quantification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/freyja /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/freyja freyja Freyja Recover relative lineage abundances from mixed SARS-CoV-2 samples from a sequencing dataset 4 58 58 24576 24576 15 15 327 327 0 0 0 0 0 0 0 0 24903 24903 73 73 +funannotate funannotate_annotate, funannotate_clean, funannotate_compare, funannotate_predict, funannotate_sort genbank, tabular, fasta, txt, gff3, json, html Funannotate is a genome prediction, annotation, and comparison software package. 2021-08-26 https://funannotate.readthedocs.io 1.8.17 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/funannotate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/funannotate funannotate funannotate funannotate is a pipeline for genome annotation (built specifically for fungi, but will also work with higher eukaryotes). 5 891 891 14118 14118 209 209 1453 1453 310 310 8597 8597 88 88 1505 1505 25673 25673 1498 1498 +fur fur fasta, txt Find unique genomic regions from target and neighbor genomes 2026-02-16 https://github.com/evolbioinf/fur 4.3 fur 4.3 Up-to-date Sequence Analysis Nucleic acid comparison Nucleic acid comparison Biomedical science Biomedical science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/fur /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/fur fur fur The program fur takes as input a set of target genome sequences and a set of related genome sequences, the neighbors. It returns the sequence regions common to all targets that are absent form the neighbors. Such regions can be used as candidate genetic markers. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gamma gamma_s, gamma tabular, gff, fasta Gene Allele Mutation Microbial Assessment 2025-08-06 https://github.com/rastanton/GAMMA @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ GAMMA 2.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gamma /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gamma 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gatk4 gatk4_mutect2, gatk4_applybqsr, gatk4_base_recalibrator, gatk4_haplotype_caller, gatk4_split_n_cigar_reads tabular, bam, txt, vcf_bgzip Genome Analysis Toolkit (GATK4) wrappers 2019-10-28 https://github.com/broadinstitute/gatk 4.6.2.0 gatk4 4.6.2.0 Up-to-date Variant Analysis, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gatk4 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gatk4 5 564 611 3976 4606 1831 2022 10954 11924 0 0 0 0 0 0 0 0 16530 14930 2633 2395 +gdcwebapp data_source_gdcwebapp auto GDCWebApp automatically filter, extract, and convert genomic data from the Genomic Data Commons portal to BED format 2017-06-23 http://bioinf.iasi.cnr.it/gdcwebapp/ 1.0.0 python To update Data Source, Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gdcwebapp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gdcwebapp 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gecko gecko csv, txt Ungapped genome comparison 2020-11-25 https://github.com/otorreno/gecko @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gecko 1.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gecko /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gecko 1 341 341 1081 1081 0 0 0 0 124 124 961 961 0 0 0 0 2042 2042 465 465 +gem_tools gem_check_memote, gem_escher_visualization, gem_extract_exchange, gem_flux_distribution, gem_flux_variability_analysis, gem_knockout, gem_phenotype_phase_plane html Tools for analyzing genome-scale metabolic models (GEMs) using COBRApy and related libraries. 2024-12-01 https://github.com/AlmaasLab/elixir-galaxy-tools-systemsbiology 0.29.1 cobra 0.21.0 To update Metabolomics, Systems Biology, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gem_tools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gem_tools 7 0 0 0 0 0 0 0 0 1 1 464 464 0 0 0 0 464 464 1 1 +gemini glimmer_acgt_content, glimmer_build_icm, glimmer_extract, glimmer_gbk_to_orf, glimmer_glimmer_to_gff, glimmer_long_orfs, glimmer_knowledge_based, glimmer_not_knowledge_based tabular, data, fasta, gff, txt Glimmer makes gene predictions. 2017-11-28 https://ccb.jhu.edu/software/glimmer/ 3.02 glimmer 3.02 Up-to-date Sequence Analysis Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/glimmer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/glimmer gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573 8 390 390 6567 6567 0 0 0 0 0 0 0 0 0 0 0 0 6567 6567 390 390 +gemini gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_db_info, gemini_@BINARY@, gemini_@BINARY@, gemini_inheritance, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@, gemini_@BINARY@ tabular, gemini.sqlite GEMINI: a flexible framework for exploring genome variation 2014-11-09 https://github.com/arq5x/gemini 0.20.1 gemini 0.30.2 To update Sequence Analysis, Next Gen Mappers Sequence analysis, Genetic variation analysis Sequence analysis, Genetic variation analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gemini /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gemini gemini GEMINI GEMINI (GEnome MINIng) is a flexible framework for exploring genetic variation in the context of the wealth of genome annotations available for the human genome. By placing genetic variants, sample phenotypes and genotypes, as well as genome annotations into an integrated database framework, GEMINI provides a simple, flexible, and powerful system for exploring genetic variation for disease and population genetics. 2 1258 1488 4490 6130 529 529 1823 1949 439 453 4187 4642 26 26 82 82 12803 10582 2496 2252 +gemma gemma tsv, interval Gemma is a genome wide association tool. 2025-05-09 https://github.com/genetics-statistics/GEMMA @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gemma 0.98.5 To update Variant Analysis, Genome-Wide Association Study iuc https://github.com/galaxyproject/tools-iuc/tree/master/tools/gemma /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gemma 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +genebed_maf_to_fasta GeneBed_Maf_Fasta2 fasta Stitch gene blocks given a set of coding exon intervals 2020-08-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/genebed_maf_to_fasta/ 1.0.1 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genebed_maf_to_fasta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genebed_maf_to_fasta 1 2 2 4 4 16 280 152 2906 0 0 0 0 0 0 0 0 2910 156 282 18 +genehunter_modscore genehunter_modscore allegro_ihaplo, allegro_fparam Maximised LOD score pedigree analysis utility 2017-11-27 https://www.unimedizin-mainz.de/imbei/biometricsgenomic-statistics-and-bioinformatics/software/genehunter-modscore-40.html?L=1 @VERSION@.0 ghm 3.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genehunter_modscore /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genehunter_modscore 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +geneiobio gene_iobio_display_generation_iframe html Gene.iobio is an interactive tool for variant and trio analysis. 2023-06-20 https://github.com/iobio/gene.iobio 4.7.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/geneiobio /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/geneiobio 1 48 48 172 172 0 0 0 0 8 8 158 158 0 0 0 0 330 330 56 56 +genetrack genetrack "Contains a tool that separately identifies peaks on the forward ""+” (W) and reverse “-” (C) strand." 2015-12-18 @WRAPPER_VERSION@.1 numpy To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genetrack /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genetrack 1 0 0 0 0 78 203 228 674 0 0 0 0 0 0 0 0 674 228 203 78 +genomescope genomescope png, txt, tabular Analyze unassembled short reads 2021-04-30 https://github.com/tbenavi1/genomescope2.0 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ genomescope2 2.1.0 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomescope /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genomescope https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 1 1029 1029 5878 5878 641 641 3149 3149 261 261 2337 2337 37 37 614 614 11978 11978 1968 1968 +genomic_super_signature genomic_super_signature csv, html Interpretation of RNAseq experiments through robust, efficient comparison to public databases 2022-01-12 https://github.com/shbrief/GenomicSuperSignature @TOOL_VERSION@+galaxy@GALAXY_VERSION@ bioconductor-genomicsupersignature 1.18.0 To update Sequence Analysis, RNA, Transcriptomics Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction Gene-set enrichment analysis, Essential dynamics, Deposition, Principal component visualisation, Dimensionality reduction RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment RNA-Seq, Transcriptomics, Microbial ecology, Genotype and phenotype, Microarray experiment iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genomic_super_signature /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genomic_super_signature genomicsupersignature GenomicSuperSignature GenomicSuperSignature is a package for the interpretation of RNA-seq experiments through robust, efficient comparison to public databases. 1 20 20 58 58 0 0 0 0 0 0 0 0 0 0 0 0 58 58 20 20 +genrich genrich encodepeak, bedgraph, bed, txt Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). 2019-07-05 https://github.com/jsh58/Genrich 0.5 genrich 0.6.1 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/genrich /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/genrich 1 283 435 2214 3829 460 460 3086 3086 31 31 700 703 0 0 0 0 7618 6000 926 774 +geopandas geopandas_table2geojson geojson GeoPandas is an open source project to make working with geospatial data easier. 2025-04-20 https://geopandas.org @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ geopandas To update Geo Science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/geopandas /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/geopandas 1 3 3 41 41 0 0 0 0 0 0 0 0 0 0 0 0 41 41 3 3 +get_hrun get_hrun vcf Annotate indel variants with homopolymer context 2021-03-02 https://github.com/galaxyproject/tools-iuc/tree/master/tools/get_hrun 0.5.9.2 pyfaidx 0.9.0.4 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/get_hrun /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/get_hrun 1 5 5 9 9 0 0 0 0 0 0 0 0 0 0 0 0 9 9 5 5 +getorganelle get_annotated_regions_from_gb, get_organelle_from_reads fasta, txt, gfa1, fastg, tsv, fastq, sam GetOrganelle - This toolkit assembles organelle genomes from genomic skimming data. 2022-03-15 https://github.com/Kinggerm/GetOrganelle 1.7.7.1 getorganelle 1.7.7.1 Up-to-date Assembly De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming De-novo assembly, Genome assembly, Mapping assembly, Mapping, Sequence trimming Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms Cell biology, Sequence assembly, Whole genome sequencing, Plant biology, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/getorganelle /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/getorganelle getorganelle GetOrganelle A fast and versatile toolkit for accurate de novo assembly of organelle genomes.This toolkit assemblies organelle genome from genomic skimming data. 2 403 403 9423 9423 0 0 0 0 108 108 1588 1588 0 0 0 0 11011 11011 511 511 +gfa_to_fa gfa_to_fa fasta gfa_to_fa - Converting GFA format to Fasta format 2019-06-18 http://gfa-spec.github.io/GFA-spec/ 0.1.2 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gfa_to_fa /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gfa_to_fa microbiome/plasmid-metagenomics-nanopore 1 911 1010 9926 11805 621 661 6768 7202 186 188 1778 1807 52 52 228 228 21042 18700 1911 1770 +gff3_rebase gff3.rebase gff3 Rebase a GFF against a parent GFF (e.g. an original genome) 2015-05-25 https://github.com/galaxyproject/tools-iuc/tree/master/tools/gff3_rebase 1.2 bcbiogff 0.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gff3_rebase /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gff3_rebase 1 80 83 1290 1337 42 45 179 207 12 12 182 182 1 1 1 1 1727 1652 141 135 +gffcompare gffcompare gtf, tabular, txt Galaxy wrappers for Geo Pertea's GffCompare package. 2017-03-27 https://github.com/gpertea/gffcompare/ 0.12.10 gffcompare 0.12.10 Up-to-date Transcriptomics Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffcompare /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gffcompare gffcompare gffcompare Program for comparing, annotating, merging and tracking transcripts in GFF files. 1 1157 1332 4195 5221 1776 2918 5168 9180 179 272 1521 2011 29 29 79 79 16491 10963 4551 3141 +gffread gffread gff3, gtf, bed, fasta, txt gffread filters and/or converts GFF3/GTF2 records 2019-10-29 http://ccb.jhu.edu/software/stringtie/gff.shtml#gffread/ @GALAXY_TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gffread 0.12.9 To update Sequence Analysis Sequence annotation Sequence annotation Nucleic acids, Sequence analysis Nucleic acids, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/gffread /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gffread gffread gffread program for filtering, converting and manipulating GFF files 1 2441 2656 16223 18398 2944 4174 18563 29048 879 923 5541 6033 107 107 998 1000 54479 41325 7860 6371 +ggplot2 ggplot2_barplot, ggplot2_boxplot, ggplot2_heatmap, ggplot2_pca, ggplot2_histogram, ggplot2_point, ggplot2_violin png, txt ggplot2 is a system for declaratively creating graphics, based on The Grammar of Graphics.You provide the data, tell ggplot2 how to map variables to aesthetics, what graphical primitives to use,and it takes care of the details. 2017-05-26 https://github.com/tidyverse/ggplot2 3.5.1 r-ggplot2 2.2.1 To update Visualization Visualisation Visualisation Data visualisation Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggplot2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ggplot2 ggplot2 ggplot2 Plotting system for R, based on the grammar of graphics. microbiome/pathogen-detection-from-nanopore-foodborne-data 7 1825 2030 28524 31954 1894 2101 31068 34254 1297 1311 10678 11132 220 220 3884 3884 81224 74154 5662 5236 +ggplot2_heatmap2 ggplot2_heatmap2 pdf heatmap.2 function from the R gplots package 2019-02-10 https://github.com/cran/gplots @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-gplots 2.17.0 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/heatmap2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/heatmap2 https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1 1 5453 6454 52101 62236 6555 8257 69586 84002 840 946 8530 9871 281 285 2996 3046 159155 133213 15942 13129 +ggupset emc-ggupset png, tabular Create Upset Plots with ggupset 2022-12-17 https://github.com/const-ae/ggupset 1.0 r-ggupset To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ggupset /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ggupset 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +goenrichment goenrichment, goslimmer tabular, png Performs GO Enrichment analysis. 2018-12-28 https://github.com/DanFaria/GOEnrichment @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ goenrichment 2.0.1 To update Genome annotation Gene-set enrichment analysis Gene-set enrichment analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goenrichment /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/goenrichment goenrichment GOEnrichment GOEnrichment is a tool for performing GO enrichment analysis of gene sets, such as those obtained from RNA-seq or Microarray experiments, to help characterize them at the functional level. It is available in Galaxy Europe and as a stand-alone tool.GOEnrichment is flexible in that it allows the user to use any version of the Gene Ontology and any GO annotation file they desire. To enable the use of GO slims, it is accompanied by a sister tool GOSlimmer, which can convert annotation files from full GO to any specified GO slim.The tool features an optional graph clustering algorithm to reduce the redundancy in the set of enriched GO terms and simplify its output.It was developed by the BioData.pt / ELIXIR-PT team at the Instituto Gulbenkian de Ciência. 2 799 928 6000 7557 1081 1196 8060 9309 230 233 1602 1647 5 6 39 44 18557 15701 2363 2115 +goseq goseq tabular, pdf, rdata goseq does selection-unbiased testing for category enrichment amongst differentially expressed (DE) genes for RNA-seq data 2016-11-12 https://bioconductor.org/packages/release/bioc/html/goseq.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-goseq 1.62.0 To update Statistics, RNA, Micro-array Analysis Gene functional annotation Gene functional annotation RNA-Seq RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/goseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/goseq goseq GOseq Detect Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data. 1 3196 3921 23708 28273 3528 4089 26762 31254 640 680 4461 5015 103 104 751 784 65326 55682 8794 7467 +gprofiler gprofiler_convert, gprofiler_gost, gprofiler_orth, gprofiler_random, gprofiler_snpense tabular, html functional enrichment analysis of gene lists, convertion between various types of namespaces, translation gene identifiers between organisms and more 2019-10-30 https://biit.cs.ut.ee/gprofiler @TOOL_VERSION@ r-gprofiler2 To update Statistics, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gprofiler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gprofiler 5 550 584 4378 4901 792 850 8647 9196 0 0 0 0 0 0 0 0 14097 13025 1434 1342 +graphembed graphembed tabular, pdf, txt Compute a 2D embedding of a data matrix given supervised class information 2019-12-10 https://github.com/fabriziocosta/GraphEmbed @VERSION@.0 graph_embed 2.4 To update Statistics, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphembed /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/graphembed 1 5 7 18 79 44 49 71 134 0 0 0 0 0 0 0 0 213 89 56 49 +graphlan graphlan, graphlan_annotate png, pdf, ps, eps, svg, phyloxml GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees 2017-03-03 https://github.com/biobakery/graphlan @WRAPPER_VERSION@ graphlan 1.1.3 To update Metagenomics, Graphics, Phylogenetics Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Phylogenetic inference, Phylogenetic tree visualisation, Phylogenetic tree editing, Taxonomic classification Metagenomics, Phylogenetics, Phylogenomics, Cladistics Metagenomics, Phylogenetics, Phylogenomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/graphlan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/graphlan graphlan GraPhlAn GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation. https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 2 799 940 11872 13928 325 325 1773 1773 202 207 1432 1470 21 21 90 90 17261 15167 1493 1347 +groot groot tabular GROOT is a tool to type Antibiotic Resistance Genes (ARGs) in metagenomic samples 2024-05-14 https://github.com/will-rowe/groot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ groot 1.1.2 To update Metagenomics Antimicrobial resistance prediction Antimicrobial resistance prediction Metagenomics, Microbiology, Genomics Metagenomics, Microbiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/groot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/groot groot GROOT Indexed variation graphs for efficient and accurate resistome profiling. 1 5 5 7 7 0 0 0 0 0 0 0 0 3 3 37 37 44 44 8 8 +gtdb_to_taxdump gtdb_to_taxdump tabular Convert GTDB taxonomy to NCBI taxdump format 2024-08-25 https://github.com/nick-youngblut/gtdb_to_taxdump 0.1.9 gtdb_to_taxdump 0.1.9 Up-to-date Metagenomics Data handling, Mapping, Generation Data handling, Mapping, Generation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdb_to_taxdump /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gtdb_to_taxdump gtdb_to_taxdump gtdb_to_taxdump Tool with multiple functions. Main functions are to create a DIAMOND database from the GTDB taxonomy data or create a NCBI taxdump format out of this data. This tool can also create a mapping between the taxonomy classification between GTDB and NCBI. 1 27 27 1127 1127 0 0 0 0 0 0 0 0 0 0 0 0 1127 1127 27 27 +gtdbtk gtdbtk_classify_wf txt GTDB-Tk is a software tool kit for assigning objective taxonomic classifications to bacterial and archaeal genomesbased on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds orthousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can alsobe applied to isolate and single-cell genomes. 2022-12-13 https://github.com/Ecogenomics/GTDBTk 2.7.2 gtdbtk 2.7.2 Up-to-date Metagenomics Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Genome alignment, Taxonomic classification, Sequence assembly, Query and retrieval Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins Metagenomics, Taxonomy, Phylogenetics, Database management, Proteins iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtdbtk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gtdbtk GTDB-Tk GTDB-Tk a toolkit to classify genomes with the Genome Taxonomy Database.GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB. It is designed to work with recent advances that allow hundreds or thousands of metagenome-assembled genomes (MAGs) to be obtained directly from environmental samples. It can also be applied to isolate and single-cell genomes. The GTDB-Tk is open source and released under the GNU General Public License (Version 3). 1 462 462 3982 3982 305 305 1566 1566 177 177 1095 1095 15 15 1439 1439 8082 8082 959 959 +gtftobed12 gtftobed12 bed12, tabular Convert GTF files to BED12 format 2018-05-17 http://genome-source.cse.ucsc.edu/gitweb/?p=kent.git;a=blob;f=src/userApps/README 357 ucsc-gtftogenepred 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gtfToBed12 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gtfToBed12 UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 3876 4805 9565 11802 3850 4091 9783 10498 436 457 2010 2130 213 214 432 460 24890 21790 9567 8375 +gubbins gubbins txt, gff3, embl, fasta, phylip, csv, vcf Gubbins - bacterial recombination detection 2017-06-22 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ gubbins 3.4.3 To update Sequence Analysis Genotyping, Phylogenetic inference, Ancestral reconstruction Genotyping, Phylogenetic inference, Ancestral reconstruction Phylogeny, Genotype and phenotype, Whole genome sequencing Phylogeny, Genotype and phenotype, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gubbins /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gubbins gubbins Gubbins Gubbins is a tool for rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences. 1 402 428 4731 5118 268 288 3847 4061 250 317 1977 2858 0 0 0 0 12037 10555 1033 920 +gvcftools gvcftools_extract_variants vcf gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.gVCF are VCF 4.1 files which follow a set of conventions for representing all sitesin the genome, further described at https://sites.google.com/site/gvcftools/home/about-gvcf. 2016-12-29 https://github.com/sequencing/gvcftools 0.1 gvcftools 0.17.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gvcftools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gvcftools 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +gwastools gwastools_manhattan_plot pdf 2019-10-07 https://bioconductor.org/packages/release/bioc/html/GWASTools.html 0.1.0 bioconductor-gwastools 1.56.0 To update Visualization, Variant Analysis Deposition, Analysis, Annotation Deposition, Analysis, Annotation GWAS study GWAS study iuc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gwastools gwastools GWASTools Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis. 1 0 0 0 0 0 0 0 0 0 0 0 0 6 6 26 26 26 26 6 6 +gwtc_analysis gwtc_analysis tabular, html GWTC catalog statistics, event selection, skymap search, and parameter-estimation reporting. 2026-03-12 https://github.com/danielsentenac/gwtc_analysis 0.4.3 gwtc_analysis To update Astronomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/gwtc_analysis /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/gwtc_analysis 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +halfdeep halfdeep bed HalfDeep: Automated detection of intervals covered at half depth by sequenced reads. 2024-11-27 https://github.com/makovalab-psu/HalfDeep 0.1.0 halfdeep 0.1.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halfdeep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/halfdeep 1 0 0 0 0 5 5 52 52 0 0 0 0 0 0 0 0 52 52 5 5 +halla halla tabular, pdf Hierarchical All-against-All association 2025-11-05 https://github.com/biobakery/halla @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ halla 0.8.40 To update Metagenomics Statistical calculation, Gene expression profiling, Essential dynamics Statistical calculation, Gene expression profiling, Essential dynamics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics Microbial ecology, Microarray experiment, Metabolomics, Phylogeny, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/halla /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/halla halla HAllA High-sensitivity pattern discovery in large, paired multi-omic datasets. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +haltools hal_hal2fasta, hal_hal2maf, hal_hal2paf, hal_hal2vg, hal_haladdtobranch, hal_halalignedextract, hal_halalignmentdepth, hal_halbranchmutations, hal_halcoverage, hal_halextract, hal_halindels, hal_halliftover, hal_hallodextract, hal_halmaskextract, hal_halpctid, hal_halremovegenome, hal_halremovesubtree, hal_halrenamegenomes, hal_halrenamesequences, hal_halreplacegenome, hal_halsnps, hal_halstats, hal_halsummarizemutations, hal_halsynteny, hal_halupdatebranchlengths, hal_halvalidate, hal_halwiggleliftover, hal_maf2hal fasta, maf, paf, hal.pg, hal, bed, wig, tabular, txt, psl A set of tools for manipulating HAL alignment files 2025-11-25 https://github.com/ComparativeGenomicsToolkit/cactus 3.1.4 cactus 2019.03.01 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/haltools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/haltools 28 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +hamronization hamronize_summarize, hamronize_tool tabular Convert AMR gene detection tool output to hAMRonization specification format. 2021-02-02 https://github.com/pha4ge/hAMRonization 1.1.4 hamronization 1.2.1 To update Sequence Analysis Data handling, Antimicrobial resistance prediction, Parsing Antimicrobial resistance prediction, Parsing Public health and epidemiology, Microbiology, Bioinformatics Public health and epidemiology, Microbiology, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hamronization /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hamronization hamronization hAMRonization Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure 2 254 254 18459 18459 1 1 20 20 1 1 21 21 6 6 191 191 18691 18691 262 262 +hapcut2 hapcut2 txt, vcf Robust and accurate haplotype assembly for diverse sequencing technologies 2022-10-20 https://github.com/vibansal/HapCUT2 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ hapcut2 1.3.4 To update Assembly Haplotype mapping, Variant classification Haplotype mapping, Variant classification galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapcut2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hapcut2 hapcut2 HapCUT2 "HapCUT2 is a maximum-likelihood-based tool for assembling haplotypes from DNA sequence reads, designed to ""just work"" with excellent speed and accuracy across a range of long- and short-read sequencing technologies.The output is in Haplotype block format described here: https://github.com/vibansal/HapCUT2/blob/master/outputformat.md" 1 0 0 0 0 0 0 0 0 6 6 131 131 0 0 0 0 131 131 6 6 +hapog hapog fasta, tsv Hapo-G - Haplotype-Aware Polishing of Genomes 2022-09-16 https://github.com/institut-de-genomique/HAPO-G @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ hapog 1.3.8 To update Assembly Genome assembly, Optimisation and refinement Genome assembly, Optimisation and refinement Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hapog /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hapog hapog Hapo-G Hapo-G is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads. It capable of incorporating phasing information from high-quality reads (short or long-reads) to polish genome assemblies and in particular assemblies of diploid and heterozygous genomes. 1 94 94 677 677 0 0 0 0 0 0 0 0 36 36 392 392 1069 1069 130 130 +happy som.py tabular, json, csv A tool to perform comparisons only based on chromosome, position, and allele identity for comparison of somatic callsets. 2022-01-25 https://github.com/Illumina/hap.py @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ hap.py 0.3.15 To update Variant Analysis Variant calling, Sequence analysis, Genotyping Variant calling, Sequence analysis, Genotyping Genomics, DNA polymorphism Genomics, DNA polymorphism iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/happy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/happy hap.py hap.py This is a set of programs based on htslib to benchmark variant calls against gold standard truth datasets.To compare a VCF against a gold standard dataset, use the following commmand line to perform genotype-level haplotype comparison. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +heinz heinz_bum, heinz, heinz_scoring, heinz_visualization txt, pdf An algorithm for identification of the optimal scoring subnetwork. 2018-06-11 https://github.com/ls-cwi/heinz 1.0 bioconductor-bionet 1.70.0 To update Transcriptomics, Visualization, Statistics, Single Cell Pathway or network analysis Pathway or network analysis Genetics, Gene expression, Molecular interactions, pathways and networks Genetics, Gene expression, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/heinz /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/heinz heinz Heinz Tool for single-species active module discovery. 4 123 160 823 1460 318 345 1490 1678 36 36 847 913 0 0 0 0 4051 3160 541 477 +hgvsparser hgvsparser csv Parsing and building variant descriptor strings compliant with the HGVS standard 2024-06-07 https://github.com/VariantEffect/hgvsParseR/tree/master @VERSION@+galaxy@GALAXY_VERSION@ r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hgvsparser /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hgvsparser 1 2 2 6353 6353 0 0 0 0 0 0 0 0 0 0 0 0 6353 6353 2 2 +hicap hicap tabular, genbank, svg Identify cap locus serotype and structure in Haemophilus influenzae assemblies 2026-03-26 https://github.com/scwatts/hicap 1.0.4 hicap 1.0.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hicap hicap hicap Identify cap locus serotype and structure in your Haemophilus influenzae assemblies. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +hicexplorer hicexplorer_chicaggregatestatistic, hicexplorer_chicdifferentialtest, hicexplorer_chicexportdata, hicexplorer_chicplotviewpoint, hicexplorer_chicqualitycontrol, hicexplorer_chicsignificantinteractions, hicexplorer_chicviewpoint, hicexplorer_chicviewpointbackgroundmodel, hicexplorer_hicadjustmatrix, hicexplorer_hicaggregatecontacts, hicexplorer_hicaverageregions, hicexplorer_hicbuildmatrix, hicexplorer_hicbuildmatrixmicroc, hicexplorer_hiccomparematrices, hicexplorer_hiccompartmentspolarization, hicexplorer_hicconvertformat, hicexplorer_hiccorrectmatrix, hicexplorer_hiccorrelate, hicexplorer_hicdetectloops, hicexplorer_hicdifferentialtad, hicexplorer_hicfindrestrictionsites, hicexplorer_hicfindtads, hicexplorer_hichyperoptDetectLoops, hicexplorer_hicinfo, hicexplorer_hicinterintratad, hicexplorer_hicmergedomains, hicexplorer_hicmergeloops, hicexplorer_hicmergematrixbins, hicexplorer_hicnormalize, hicexplorer_hicpca, hicexplorer_hicplotaverageregions, hicexplorer_hicplotdistvscounts, hicexplorer_hicplotmatrix, hicexplorer_hicplotsvl, hicexplorer_hicplotviewpoint, hicexplorer_hicquickqc, hicexplorer_hicsummatrices, hicexplorer_hictransform, hicexplorer_hicvalidatelocations h5, tar.gz, interval, txt, png, tabular, zip, bam, html, cool, npz, mcool, bedgraph, bed, gff HiCExplorer: Set of programs to process, analyze and visualize Hi-C data. 2017-08-24 https://github.com/deeptools/HiCExplorer 3.7.6 hicexplorer 3.7.6 Up-to-date Sequence Analysis, Visualization bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicexplorer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hicexplorer https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 39 354 633 40441 75024 55 55 2146 2146 27 27 5559 5584 1 1 2 2 82756 48148 716 437 +hicstuff hicstuff_pipeline tabular, cool A toolkit to generate and manipulate Hi-C matrices 2022-11-25 https://github.com/koszullab/hicstuff 3.2.5 hicstuff 3.2.5 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hicstuff /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hicstuff 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +hifiasm hifiasm gfa1, txt A fast haplotype-resolved de novo assembler 2024-07-11 https://github.com/chhylp123/hifiasm @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ hifiasm 0.25.0 To update Assembly bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hifiasm https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 1 803 803 2713 2713 585 585 2136 2136 187 187 3817 3817 51 51 183 183 8849 8849 1626 1626 +hifiasm_meta hifiasm_meta A hifiasm fork for metagenome assembly using Hifi reads. 2023-01-18 https://github.com/xfengnefx/hifiasm-meta 0.3.1 hifiasm_meta hamtv0.3.1 To update Metagenomics Sequence assembly Sequence assembly Sequence assembly, Metagenomics Sequence assembly, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/hifiasm_meta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hifiasm_meta hifiasm-meta Hifiasm-meta Hifiasm_meta - de novo metagenome assembler, based on hifiasm, a haplotype-resolved de novo assembler for PacBio Hifi reads. 1 40 40 229 229 0 0 0 0 16 16 368 368 0 0 0 0 597 597 56 56 +hisat2 hisat2 bam, fastqsanger, txt, tabular HISAT2 is a fast and sensitive spliced alignment program. 2015-09-29 http://ccb.jhu.edu/software/hisat2/ 2.2.2 hisat2 2.2.2 Up-to-date Assembly Sequence alignment Sequence alignment RNA-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hisat2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hisat2 hisat2 HISAT2 Alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome). https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f 1 12585 14119 420921 467443 28716 40390 729970 1057729 5266 6509 88398 111027 1273 1277 52049 52136 1688335 1291338 62295 47840 +hivclustering hivclustering hivtrace Infers transmission networks from pairwise distances inferred by tn93 2018-06-06 https://pypi.org/project/hivclustering/ 1.3.1 python-hivclustering 1.8.0 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hivclustering /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hivclustering 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +hmmer3 hmmer_alimask, hmmer_hmmalign, hmmer_hmmbuild, hmmer_hmmconvert, hmmer_hmmemit, hmmer_hmmfetch, hmmer_hmmscan, hmmer_hmmsearch, hmmer_jackhmmer, hmmer_nhmmer, hmmer_nhmmscan, hmmer_phmmer stockholm, hmm3, fasta HMMER is used for searching sequence databases for homologs of proteinsequences, and for making protein sequence alignments. It implementsmethods using probabilistic models called profile hidden Markov models(profile HMMs). 2015-02-16 http://hmmer.org/ 3.4 hmmer 3.4 Up-to-date Sequence Analysis Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Sequence generation, Data retrieval, Statistical calculation, Database search, Formatting, Database search, Database search, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Database search, Sequence database search Formatting, Multiple sequence alignment, Sequence profile generation, Format validation, Conversion, Data retrieval, Statistical calculation, Formatting, Probabilistic sequence generation, Statistical calculation, Statistical calculation, Sequence database search, Formatting, Sequence database search, Sequence database search Sequence analysis, Sequence sites, features and motifs, Gene and protein families Sequence analysis, Sequence sites, features and motifs, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hmmer3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hmmer3 hmmer3 HMMER3 This tool is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models. The new HMMER3 project, HMMER is now as fast as BLAST for protein search. 12 380 403 36302 43262 0 0 0 0 83 84 4731 4887 97 97 540 543 48692 41573 584 560 +htseq_count htseq_count tabular, bam Count aligned reads (SAM/BAM) that overlap genomic features (GFF) 2016-09-15 https://readthedocs.org/projects/htseq/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ htseq 2.1.2 To update Genomic Interval Operations, SAM, Sequence Analysis, RNA Nucleic acid sequence analysis Nucleic acid sequence analysis Sequence analysis Sequence analysis lparsons https://github.com/galaxyproject/tools-iuc/tree/main/tools/htseq_count /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/htseq_count htseq HTSeq Python framework to process and analyse high-throughput sequencing (HTS) data 1 3989 5200 135497 191189 11193 18984 254054 434409 2158 3031 21954 36591 552 555 16740 16789 678978 428245 27770 17892 +humann humann, humann_barplot, humann_join_tables, humann_reduce_table, humann_regroup_table, humann_rename_table, humann_renorm_table, humann_split_stratified_table, humann_split_table, humann_unpack_pathways tabular, biom1, txt, sam, fasta, png, pdf, svg HUMAnN for functionally profiling metagenomes and metatranscriptomes at species-level resolution 2021-05-12 http://huttenhower.sph.harvard.edu/humann 3.9 humann 3.9 Up-to-date Metagenomics Species frequency estimation, Taxonomic classification, Phylogenetic analysis Species frequency estimation, Taxonomic classification, Phylogenetic analysis Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/humann /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/humann humann humann HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads). This process, referred to as functional profiling, aims to describe the metabolic potential of a microbial community and its members. More generally, functional profiling answers the question “What are the microbes in my community-of-interest doing (or are capable of doing)?” https://usegalaxy.eu/published/workflow?id=b14845359b702444 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short 10 795 795 52483 52483 123 123 3171 3171 122 122 4812 4812 17 17 987 987 61453 61453 1057 1057 +hybpiper hybpiper fasta, tar, txt Analyse targeted sequence capture data 2023-08-30 https://github.com/mossmatters/HybPiper 2.1.6 hybpiper 2.3.4 To update Sequence Analysis, Phylogenetics Sequence trimming, Sequence assembly, Read mapping Sequence trimming, Sequence assembly, Read mapping Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics Phylogenetics, Plant biology, Gene transcripts, Sequence assembly, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hybpiper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hybpiper HybPiper HybPiper Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).Recovering genes from targeted sequence capture data.Current version: 1.3.1 (August 2018).-- Read our article in Applications in Plant Sciences (Open Access).HybPiper was designed for targeted sequence capture, in which DNA sequencing libraries are enriched for gene regions of interest, especially for phylogenetics. HybPiper is a suite of Python scripts that wrap and connect bioinformatics tools in order to extract target sequences from high-throughput DNA sequencing reads. 1 9 9 1679 1679 0 0 0 0 6 6 258 258 0 0 0 0 1937 1937 15 15 +hyphy hyphy_absrel, hyphy_annotate, hyphy_b_still, hyphy_bgm, hyphy_busted, hyphy_cfel, hyphy_cln, hyphy_conv, hyphy_fade, hyphy_fel, hyphy_fubar, hyphy_gard, hyphy_infer_stasis_clusters, hyphy_meme, hyphy_prime, hyphy_relax, hyphy_slac, hyphy_sm19, hyphy_strike_ambigs markdown, hyphy_results.json, nhx, nex, fasta, json, txt Hypothesis Testing using Phylogenies 2018-06-08 http://www.hyphy.org 2.5.96 hyphy 2.5.100 To update Phylogenetics Statistical calculation Statistical calculation Phylogeny, Small molecules, Molecular interactions, pathways and networks Phylogeny, Small molecules, Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hyphy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hyphy HyPhy HyPhy Software package for the analysis of genetic sequences using techniques in phylogenetics, molecular evolution, and machine learning. 19 88 94 10953 11906 78 108 4725 8358 33 42 815 909 3 5 22 27 21200 16515 249 202 +hypo hypo fasta, txt Super Fast & Accurate Polisher for Long Read Genome Assemblies 2021-11-15 https://github.com/kensung-lab/hypo 1.0.3 hypo 1.0.3 Up-to-date Assembly Optimisation and refinement, Genome assembly Optimisation and refinement, Genome assembly Sequence assembly, Genomics Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/hypo /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/hypo HyPo HyPo HyPo, a Hybrid Polisher, utilizes short as well as long reads within a single run to polish a long reads assembly of small and large genomes. 1 107 107 575 575 0 0 0 0 0 0 0 0 0 0 0 0 575 575 107 107 +icescreen icescreen tabular, txt, genbank.gz, gff3.gz, embl.gz, tar.gz, gz identification of ICEs and IMEs in Bacillota genomes. 2022-01-04 https://forgemia.inra.fr/ices_imes_analysis/icescreen 1.3.3 icescreen 1.3.3 Up-to-date Genome annotation Database search, Protein feature detection Database search, Protein feature detection Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation Mobile genetic elements, Sequence sites, features and motifs, Genomics, Molecular interactions, pathways and networks, Structural variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/icescreen /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/icescreen icescreen ICEscreen A tool to detect Firmicute ICEs and IMEs, isolated or enclosed in composite structures. 1 3 3 153 153 4 4 15 15 0 0 0 0 0 0 0 0 168 168 7 7 +idba idba_hybrid, idba_tran, idba_ud fasta Wrappers for the idba assembler variants. 2018-04-26 https://i.cs.hku.hk/~alse/hkubrg/projects/index.html @IDBA_VERSION@ idba 1.1.3 To update Assembly Sequence assembly Sequence assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idba_ud /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/idba_ud idba IDBA A short read assembler based on iterative De Bruijn graph. It is developed under 64-bit Linux, but should be suitable for all unix-like system. 3 106 126 944 1353 146 169 1199 1700 0 0 0 0 1 1 3 3 3056 2146 296 253 +idr idr bed, png Galaxy wrappers for the IDR package from Nathan Boleu 2017-08-21 https://github.com/nboley/idr @VERSION@ idr 2.0.4.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/idr 1 124 147 2665 3214 209 231 1828 2058 0 0 0 0 0 0 0 0 5272 4493 378 333 +idr_download_by_ids idr_download_by_ids txt, tar Image Data Resource downloading tool 2020-02-04 https://idr.openmicroscopy.org 0.45 omero-py 5.11.1 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/idr_download /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/idr_download 1 37 46 232 457 0 0 0 0 1 1 445 445 0 0 0 0 902 677 47 38 +iedb_api iedb_api tabular Get epitope binding predictions from IEDB-API 2020-02-26 https://tools.iedb.org/main/tools-api/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Data Source, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iedb_api /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/iedb_api 1 38 43 3543 4425 6 6 33 33 3 3 234 234 0 0 0 0 4692 3810 52 47 +infercnv infercnv tabular Infer Copy Number Variation from Single-Cell RNA-Seq Data 2024-07-23 https://github.com/broadinstitute/infercnv 1.26.0 bioconductor-infercnv 1.26.0 Up-to-date Transcriptomics, Variant Analysis, Single Cell Heat map generation, Expression analysis, RNA-Seq analysis, Copy number variation detection, Clustering Heat map generation, RNA-Seq analysis, Copy number variation detection, Clustering iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/infercnv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/infercnv infercnv InferCNV Inferring copy number alterations from tumor single cell RNA-Seq data 1 7 7 31 31 0 0 0 0 0 0 0 0 0 0 0 0 31 31 7 7 +instrain instrain_compare, instrain_profile tabular, pdf, zip InStrain is a tool for analysis of co-occurring genome populations from metagenomes 2021-08-11 https://instrain.readthedocs.io/ 1.5.3 instrain 1.10.0 To update Metagenomics SNP detection, Genome comparison SNP detection, Genome comparison Mapping, Metagenomics Mapping, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/instrain /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/instrain instrain InStrain InStrain is a tool for analysis of co-occurring genome populations from metagenomes that allows highly accurate genome comparisons, analysis of coverage, microdiversity, and linkage, and sensitive SNP detection with gene localization and synonymous non-synonymous identification 2 22 22 208 208 0 0 0 0 0 0 0 0 0 0 0 0 208 208 22 22 +integronfinder integron_finder txt, tsv """IntegronFinder identify integrons with high accuracy and sensitivity.It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching""" 2022-09-22 https://github.com/gem-pasteur/Integron_Finder 2.0.5 integron_finder 2.0.6 To update Sequence Analysis Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Nucleic acid feature detection, Sequence motif recognition, Protein feature detection, Genome annotation Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis Functional genomics, Mobile genetic elements, Molecular biology, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/integron_finder /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/integron_finder integron_finder Integron Finder A tool to detect Integron in DNA sequences. 1 390 390 64428 64428 252 252 7167 7167 132 132 12061 12061 34 34 2504 2504 86160 86160 808 808 +intermine_galaxy_exchange galaxy_intermine_exchange intermine_tabular InterMine Exporter 2018-07-01 https://github.com/intermine 0.0.1 coreutils 8.25 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/intermine_galaxy_exchange /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/intermine_galaxy_exchange 1 7 14 15 53 10 17 21 90 1 1 159 159 0 0 0 0 302 195 32 18 +interproscan interproscan tabular, xml, gff3, json Interproscan queries the interpro database and provides annotations. 2021-11-15 http://www.ebi.ac.uk/Tools/pfa/iprscan5/ 5.59-91.0 interproscan 5.59_91.0 To update Sequence Analysis Sequence motif recognition, Protein feature detection Sequence motif recognition, Protein feature detection Gene and protein families, Sequence analysis Gene and protein families, Sequence analysis bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/interproscan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/interproscan interproscan_ebi InterProScan (EBI) Scan sequences against the InterPro protein signature databases. 1 2350 2550 44154 69658 486 486 3914 3914 799 804 13188 13204 144 144 9435 9435 96211 70691 3984 3779 +interval2maf Interval2Maf1 maf Extract MAF blocks given a set of intervals 2020-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.1 bx-python 0.14.0 To update Genomic Interval Operations Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/interval2maf /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/interval2maf bx-python bx-python Tools for manipulating biological data, particularly multiple sequence alignments. 1 6 10 21 107 82 1259 711 19652 2 2 23 31 1 1 7 7 19797 762 1272 91 +intervene intervene_pairwise, intervene_upset pdf, txt Create pairwise and upset plots 2018-09-11 https://intervene.readthedocs.io 0.6.5 intervene 0.6.5 Up-to-date Statistics Sequence comparison, Sequence visualisation Sequence comparison, Sequence visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/intervene /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/intervene intervene Intervene Tool for intersection and visualization of multiple gene or genomic region sets. Intervene contains three modules: venn to generate Venn diagrams of up to six sets, upset to generate UpSet plots of multiple sets, and pairwise to compute and visualize intersections of multiple sets as clustered heat maps. 2 270 284 1959 2152 274 295 4435 4873 0 0 0 0 0 0 0 0 7025 6394 579 544 +ipfp_normalisation ipfp_norm tsv Normalisation algorithm used to adjust matrices iteratively to satisfy specific row and column sum constraints while preserving the data structure. 2025-01-28 https://isoquac.net/ 0.1.0 numpy To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ipfp_normalisation /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ipfp_normalisation 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +iqtree iqtree nhx, mldist, nex, iqtree, data, txt Efficient phylogenomic software by maximum likelihood 2017-09-26 http://www.iqtree.org/ 2.4.0 iqtree 3.1.2 To update Phylogenetics Phylogenetic analysis, Sequence analysis Phylogenetic analysis, Sequence analysis Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iqtree /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/iqtree iqtree iqtree A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time 1 2588 2695 44137 45132 2814 3035 34112 35898 1165 1337 16490 18756 17 17 229 229 100015 94968 7084 6584 +irissv irissv vcf Refine insertion sequences 2021-01-17 https://github.com/mkirsche/Iris 1.0.5 samtools 1.23.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/irissv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/irissv 1 8 8 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 8 8 +irma irma txt Iterative Refinement Meta-Assembler (IRMA) is a tool to construct assembly of highly variable RNA viruses. 2024-11-09 https://wonder.cdc.gov/amd/flu/irma/irma.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ irma 1.3.4 To update Sequence Analysis Mapping assembly Mapping assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/irma /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/irma irma-virus IRMA Iterative Refinement Meta-Assembler for robust assembly, variant calling, and phasing of highly variable RNA virus sequencing data 1 12 12 16450 16450 0 0 0 0 0 0 0 0 0 0 0 0 16450 16450 12 12 +isoformswitchanalyzer isoformswitchanalyzer tabular, rdata, fasta, pdf Statistical identification of isoform switching from RNA-seq derived quantification of novel and/or annotated full-length isoforms. 2022-12-17 https://bioconductor.org/packages/devel/bioc/html/IsoformSwitchAnalyzeR.html 1.20.0 bioconductor-isoformswitchanalyzer 2.10.0 To update Transcriptomics, RNA, Statistics Sequence comparison, Sequence analysis Sequence comparison, Sequence analysis Computational biology, Gene transcripts Computational biology, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/isoformswitchanalyzer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/isoformswitchanalyzer IsoformSwitchAnalyzeR IsoformSwitchAnalyzeR Enables identification of isoform switches with predicted functional consequences from RNA-seq data. Consequences can be chosen from a long list but includes protein domains gain/loss changes in NMD sensitivity etc. It directly supports import of data from Cufflinks/Cuffdiff, Kallisto, Salmon and RSEM but other transcript qunatification tools are easy to import as well. 1 107 107 2460 2460 126 126 2434 2434 21 21 1287 1287 2 2 12 12 6193 6193 256 256 +ivar ivar_consensus, ivar_filtervariants, ivar_removereads, ivar_trim, ivar_variants fasta, tabular, bam, vcf iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing 2020-03-21 https://github.com/andersen-lab/ivar 1.4.4 ivar 1.4.4 Up-to-date Sequence Analysis Primer removal Primer removal Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ivar /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ivar andersen-lab_ivar iVar iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. 5 1081 1087 1414011 1417441 1310 1330 147224 148408 374 379 43473 54915 19 19 7502 7502 1628266 1612210 2815 2784 +iwtomics iwtomics_loadandplot, iwtomics_plotwithscale, iwtomics_testandplot rdata, tabular, pdf, txt Interval-Wise Testing for Omics Data 2017-06-08 https://bioconductor.org/packages/release/bioc/html/IWTomics.html 1.0.0 bioconductor-iwtomics 1.34.1 To update Statistics Differential gene expression analysis, Differentially-methylated region identification, Peak calling, Genome annotation, Comparison Differential gene expression analysis, Peak calling, Genome annotation, Comparison Statistics and probability Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/iwtomics /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/iwtomics iwtomics IWTomics "Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in ""Omics"" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset." 3 9 13 644 760 14 34 32 252 5 5 478 518 0 0 0 0 1530 1154 52 28 +jasminesv jasminesv vcf Merge structural variants across samples 2021-01-17 https://github.com/mkirsche/Jasmine/ 1.0.11 jasminesv 1.1.5 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jasminesv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jasminesv 1 15 15 94 94 25 25 62 62 0 0 0 0 0 0 0 0 156 156 40 40 +jbrowse jbrowse_to_standalone, jbrowse html JBrowse Genome Browser integrated as a Galaxy Tool 2015-05-01 https://jbrowse.org 1.16.11 jbrowse 1.16.11 Up-to-date Sequence Analysis Genome visualisation Genome visualisation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jbrowse jbrowse JBrowse Slick, speedy genome browser with a responsive and dynamic AJAX interface for visualization of genome data. Being developed by the GMOD project as a successor to GBrowse. https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573 2 6793 7423 26043 28614 7372 7751 22125 23288 3208 4288 18197 22221 299 300 1697 1712 75835 68062 19762 17672 +jbrowse2 jbrowse2 html JBrowse2 Genome Browser integrated as a Galaxy Tool 2021-09-30 https://jbrowse.org 3.7.0 jbrowse2 4.3.0 To update Sequence Analysis Genome visualisation, Structure visualisation, Pathway visualisation Genome visualisation, Structure visualisation, Pathway visualisation Mapping, Structural variation, Genomics, Gene structure, Sequence assembly Mapping, Structural variation, Genomics, Gene structure, Sequence assembly fubar https://github.com/galaxyproject/tools-iuc/tree/main/tools/jbrowse2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jbrowse2 jbrowse_2 JBrowse 2 Modular genome browser with views of synteny and structural variation. 1 626 626 3765 3765 349 349 1248 1248 95 95 603 603 0 0 0 0 5616 5616 1070 1070 +jcvi_gff_stats jcvi_gff_stats txt, pdf Compute statistics from a genome annotation in GFF3 format (using JCVI Python utilities) 2018-07-31 https://github.com/tanghaibao/jcvi 0.8.4 jcvi 1.6.6 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jcvi_gff_stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jcvi_gff_stats 1 761 859 3063 3622 833 902 2694 2899 611 616 1558 1578 49 49 439 439 8538 7754 2426 2254 +jdeskew jdeskew txt Deskew document images using Adaptive Radial Projection on the Fourier Magnitude Spectrum 2026-05-06 https://github.com/phamquiluan/jdeskew 0.3.0 jdeskew To update Imaging iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jdeskew /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jdeskew 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +jellyfish jellyfish jellyfish, txt, fasta, tsv Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA 2021-04-07 https://github.com/gmarcais/Jellyfish @WRAPPER_VERSION@+@VERSION_SUFFIX@ kmer-jellyfish 2.3.1 To update Assembly k-mer counting k-mer counting Sequence analysis, Genomics Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jellyfish /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jellyfish Jellyfish Jellyfish A command-line algorithm for counting k-mers in DNA sequence. 1 369 369 4901 4901 0 0 0 0 87 87 1492 1492 35 35 1519 1519 7912 7912 491 491 +join_files_by_id join_files_by_id tabular This tool will join datasets according to a column with identifier 2017-05-31 https://github.com/galaxyproject/tools-iuc/tree/master/tools/join_files_by_id 1.0 r-data.table 1.11.6 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/join_files_by_id /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/join_files_by_id 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +jq jq json jq is a lightweight and flexible command-line JSON processor 2017-06-22 https://jqlang.org/ 1.8.2 jq 1.5 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jq 1 65 72 510 2396 87 95 659 722 14 14 388 388 3 3 8 8 3514 1565 184 169 +jvarkit jvarkit_wgscoverageplotter png Jvarkit : Java utilities for Bioinformatics 2021-02-11 https://lindenb.github.io/jvarkit/ @TOOL_VERSION@ jvarkit-wgscoverageplotter 20201223 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/jvarkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/jvarkit 1 748 748 10984 10984 1487 1487 15150 15150 0 0 0 0 0 0 0 0 26134 26134 2235 2235 +kaiju kaiju_addtaxonnames, kaiju_mergeoutputs, kaiju_kaiju, kaiju_kaiju2krona, kaiju_kaiju2table tabular taxonomic classification of high-throughput sequencing reads 2025-04-22 https://github.com/bioinformatics-centre/kaiju 1.10.1 kaiju 1.10.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kaiju /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kaiju kaiju Kaiju Program for the taxonomic assignment of high-throughput sequencing reads, e.g., Illumina or Roche/454, from whole-genome sequencing of metagenomic DNA. Reads are directly assigned to taxa using the NCBI taxonomy and a reference database of protein sequences from Bacteria, Archaea, Fungi, microbial eukaryotes and viruses. 5 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 +kallisto kallisto_pseudo, kallisto_quant tabular, h5, bam kallisto is a program for quantifying abundances of transcripts from RNA-Seqdata, or more generally of target sequences using high-throughput sequencingreads. It is based on the novel idea of pseudoalignment for rapidlydetermining the compatibility of reads with targets, without the need foralignment. 2017-08-04 https://pachterlab.github.io/kallisto/ 0.48.0 kallisto 0.52.0 To update Transcriptomics Gene expression profiling Gene expression profiling Transcriptomics, RNA-Seq, Gene expression Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kallisto /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kallisto kallisto kallisto A program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. https://usegalaxy.eu/published/workflow?id=fd90652d475ed739 2 892 996 31647 35827 2181 2848 76773 93407 210 242 6155 7133 17 17 564 564 136931 115139 4103 3300 +kc_align kc-align fasta, txt Kc-Align custom tool 2020-02-20 https://github.com/davebx/kc-align @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kcalign 1.0.2 To update Sequence Analysis Multiple sequence alignment Multiple sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kc-align /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kc-align kc-align kc-align A fast and accurate tool for performing codon-aware multiple sequence alignments. Kc-Align is a codon-aware multiple aligner that uses Kalgin2 to produce in-frame gapped codon alignments for selection analysis of small genomes (mostly viral and some smaller bacterial genomes). Takes nucleotide seqeunces as inputs, converts them to their in-frame amino acid sequences, performs multiple alignment with Kalign, and then converts the alignments back to their original codon sequence while preserving the gaps. Produces three outputs: the gapped nucleotide alignments in FASTA format and in CLUSTAL format and the amino acid level alignment.Kc-Align will also attempt to detect any frameshift mutations in the input reads. If a frameshift is detected, that sequence will not be included in the multiple alignment and its ID will be printed to stdout. 1 51 57 243 385 263 295 7653 8360 0 0 0 0 0 0 0 0 8745 7896 352 314 +kegg_pathways_completeness kegg_pathways_completeness tsv Compute KEGG pathway/module completeness from KOs or per-contig annotation 2025-12-05 https://github.com/EBI-Metagenomics/kegg-pathways-completeness-tool @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kegg-pathways-completeness 1.4.3 To update Metagenomics, Assembly, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kegg_pathways_completeness /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kegg_pathways_completeness 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +khmer khmer_abundance_distribution_single, khmer_abundance_distribution, khmer_count_median, khmer_partition, khmer_extract_partitions, khmer_filter_abundance, khmer_filter_below_abundance_cutoff, khmer_normalize_by_median oxlicg, csv, txt In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more 2015-03-24 https://khmer.readthedocs.org/ 3.0.0a3 khmer 3.0.0a3 Up-to-date Assembly, Next Gen Mappers Standardisation and normalisation, De-novo assembly Standardisation and normalisation, De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/khmer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/khmer khmer khmer khmer is a set of command-line tools for working with DNA shotgun sequencing data from genomes, transcriptomes, metagenomes, and single cells. khmer can make de novo assemblies faster, and sometimes better. khmer can also identify (and fix) problems with shotgun data. 8 98 116 1572 2262 169 185 1179 1564 25 25 2179 2179 0 0 0 0 6005 4930 326 292 +king king txt Kinship-based INference for Gwas 2021-11-16 http://people.virginia.edu/~wc9c/KING/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ king 2.3.2 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/king /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/king 1 8 8 16 16 0 0 0 0 0 0 0 0 0 0 0 0 16 16 8 8 +kleborate kleborate tabular Screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) 2022-09-09 https://github.com/katholt/Kleborate @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kleborate 3.2.4 To update Metagenomics Multilocus sequence typing, Genome assembly, Virulence prediction Multilocus sequence typing, Genome assembly, Virulence prediction Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing Public health and epidemiology, Metagenomics, Population genomics, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kleborate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kleborate kleborate Kleborate Genomic surveillance framework and global population structure for Klebsiella pneumoniae.Kleborate is a tool to screen genome assemblies of Klebsiella pneumoniae and the Klebsiella pneumoniae species complex (KpSC) for:.A manuscript describing the Kleborate software in full is currently in preparation. In the meantime, if you use Kleborate, please cite the preprint: Lam, MMC. et al. Genomic surveillance framework and global population structure for Klebsiella pneumoniae. bioRxiv (2020). 1 123 123 1479 1479 0 0 0 0 0 0 0 0 0 0 0 0 1479 1479 123 123 +kma kma_map tabular, txt, fasta Map with KMA 2019-10-30 https://bitbucket.org/genomicepidemiology/kma 1.6.11 kma 1.6.11 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kma /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kma 1 2 2 5 5 0 0 0 0 0 0 0 0 0 0 0 0 5 5 2 2 +kmer2stats kmer2stats tabular A tool for creating data files for statistics based on kmers 2025-04-16 https://github.com/SantaMcCloud/kmer2stats @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kmer2stats 1.0.3 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmer2stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kmer2stats 1 8 8 310 310 0 0 0 0 0 0 0 0 0 0 0 0 310 310 8 8 +kmindex kmindex_build, kmindex_query kmindex Index and query k-mers from sequencing samples using Bloom filters 2025-12-10 https://github.com/tlemane/kmindex 0.6.0 kmindex 0.6.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kmindex /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kmindex kmindex kmindex kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kneaddata kneaddata txt Quality control and contaminant removal for metagenomic data 2026-02-04 https://github.com/biobakery/kneaddata 0.12.1 kneaddata 0.12.4 To update Metagenomics, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kneaddata /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kneaddata 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +kofamscan kofamscan txt, zip Gene function annotation tool based on KEGG Orthology and hidden Markov model 2020-11-12 https://github.com/takaram/kofam_scan @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ kofamscan 1.3.0 To update Sequence Analysis Sequence analysis, Gene functional annotation Sequence analysis, Gene functional annotation Genomics, Structure analysis Genomics, Structure analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kofamscan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kofamscan kofamscan kofamscan KofamScan is a gene function annotation tool based on KEGG Orthology and hidden Markov model. You need KOfam database to use this tool. 1 94 94 2904 2904 0 0 0 0 0 0 0 0 2 2 3 3 2907 2907 96 96 +kraken kraken-filter, kraken-mpa-report, kraken-report, kraken-translate, kraken tabular Kraken is a system for assigning taxonomic labels to short DNAsequences, usually obtained through metagenomic studies. Previous attempts by otherbioinformatics software to accomplish this task have often used sequence alignmentor machine learning techniques that were quite slow, leading to the developmentof less sensitive but much faster abundance estimation programs. Kraken aims toachieve high sensitivity and high speed by utilizing exact alignments of k-mersand a novel classification algorithm. 2017-01-24 http://ccb.jhu.edu/software/kraken/ @WRAPPER_VERSION@ kraken 1.1.1 To update Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics Taxonomy, Metagenomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/kraken kraken Kraken System for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. It aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. 5 1452 1453 75318 75385 2535 4229 59050 144905 904 1133 38078 44609 114 114 3720 3720 268619 176166 6929 5005 +kraken2 kraken2 tabular Kraken2 for taxonomic designation. 2019-03-05 http://ccb.jhu.edu/software/kraken/ 2.17.1 kraken2 2.17.1 Up-to-date Metagenomics Taxonomic classification Taxonomic classification Taxonomy, Metagenomics, Microbial ecology, Microbiology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/kraken2/kraken2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/kraken2/kraken2 kraken2 kraken2 Kraken 2 is the newest version of Kraken, a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. This classifier matches each k-mer within a query sequence to the lowest common ancestor (LCA) of all genomes containing the given k-mer. The k-mer assignments inform the classification algorithm.Any assumption that Kraken’s raw read assignments can be directly translated into species or strain-level abundance estimates is flawed. Bracken (Bayesian Reestimation of Abundance after Classification with KrakEN), estimates species abundances in metagenomics samples by probabilistically re-distributing reads in the taxonomic tree. (Lu, Jennifer et al. “Bracken: estimating species abundance in metagenomics data.”) https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling 1 9806 9999 519669 530279 7561 7562 224146 224149 2412 2459 87806 88898 216 216 26628 26628 869954 858249 20236 19995 +kraken_biom kraken_biom tabular, mothur.map Create BIOM-format tables (http://biom-format.org) from Kraken output (http://ccb.jhu.edu/software/kraken/) 2022-09-03 https://github.com/smdabdoub/kraken-biom 1.2.0 kraken-biom 1.2.0 Up-to-date Metagenomics Genome annotation, Taxonomic classification Genome annotation, Taxonomic classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_biom /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kraken_biom kraken-biom kraken-biom Create BIOM-format tables from Kraken output microbiome/taxonomic-profiling 1 857 857 4747 4747 47 47 150 150 95 95 963 963 9 9 17 17 5877 5877 1008 1008 +kraken_taxonomy_report kraken_taxonomy_report tabular, txt Kraken taxonomy report 2016-06-01 https://github.com/blankenberg/Kraken-Taxonomy-Report @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ biopython 1.70 To update Metagenomics Visualisation, Classification Visualisation, Classification Metagenomics, Taxonomy Metagenomics, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/kraken_taxonomy_report /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/kraken_taxonomy_report Kraken-Taxonomy-Report Kraken-Taxonomy-Report view report of classification for multiple samples 1 1148 1155 5719 5735 1291 1717 5613 7684 148 148 587 587 10 10 25 25 14031 11944 3030 2597 +krakentools krakentools_alpha_diversity, krakentools_beta_diversity, krakentools_combine_kreports, krakentools_extract_kraken_reads, krakentools_kreport2krona, krakentools_kreport2mpa txt, tabular, fasta.gz KrakenTools is a suite of scripts to be used alongside the Kraken 2023-01-13 https://github.com/jenniferlu717/KrakenTools 1.2.1 krakentools 1.2.1 Up-to-date Metagenomics Visualisation, Aggregation Visualisation, Aggregation Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/krakentools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/krakentools krakentools KrakenTools KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b14845359b702444 microbiome/beer-data-analysis, microbiome/diversity, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling 6 2603 2603 161915 161915 1861 1861 40010 40010 488 488 18602 18602 64 64 5824 5824 226351 226351 5016 5016 +krocus krocus tabular, fastq Predict MLST directly from uncorrected long reads 2019-09-03 https://github.com/quadram-institute-bioscience/krocus 1.0.1 krocus 1.0.3 To update Sequence Analysis Multilocus sequence typing, k-mer counting Multilocus sequence typing, k-mer counting Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/krocus /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/krocus krocus krocus Predict MLST directly from uncorrected long reads 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +last last_al, last_db, last_split, last_train, last_maf_convert maf, lastdb, txt LAST finds similar regions between sequences. 2020-06-17 http://last.cbrc.jp/ 1205 last 1651 To update Sequence Analysis Sequence alignment Sequence alignment Genomics, Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/last /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/last last LAST Short read alignment program incorporating quality scores 5 40 43 316 384 0 0 0 0 0 0 0 0 3 3 22 22 406 338 46 43 +lastz lastz_wrapper_2, lastz_d_wrapper tabular, png, txt Galaxy wrappers for the Lastz and Lastz_d 2018-02-12 https://github.com/lastz/lastz 1.04.52 lastz 1.04.52 Up-to-date Next Gen Mappers Sequence alignment, Read mapping Sequence alignment, Read mapping Genomics Genomics devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/lastz /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lastz lastz LASTZ A tool for (1) aligning two DNA sequences, and (2) inferring appropriate scoring parameters automatically. 2 493 570 57942 85720 758 3548 154432 208919 149 206 14671 39255 13 14 4663 4664 338558 231708 4338 1413 +lcrgenie lcrgenie xlsx Ligase Chain Reaction Genie 2022-12-02 https://github.com/neilswainston/LCRGenie @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ lcr_genie To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lcrgenie /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lcrgenie 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +legsta legsta tabular Performs in silico Legionella pneumophila sequence based typing. 2022-02-21 https://github.com/tseemann/legsta 0.5.2 legsta 0.5.2 Up-to-date Sequence Analysis Sequence analysis Sequence analysis Public health and epidemiology Public health and epidemiology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/legsta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/legsta legsta legsta Performs in silico Legionella pneumophila sequence based typing 1 13 13 134 134 0 0 0 0 0 0 0 0 0 0 0 0 134 134 13 13 +length_and_gc_content length_and_gc_content tabular Gets gene length and gc content from a fasta and a GTF file 2016-11-13 https://github.com/galaxyproject/tools-iuc/tree/master/tools/length_and_gc_content 0.1.2 r-optparse 1.3.2 To update Fasta Manipulation, Statistics, RNA, Micro-array Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/length_and_gc_content /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/length_and_gc_content 1 973 1056 4962 5219 1265 1410 2651 3077 123 123 317 317 8 8 14 14 8627 7944 2597 2369 +lexicmap lexicmap_index, lexicmap_search lexicmap_index, tsv, tabular LexicMap is a nucleotide sequence alignment tool for efficiently querying genomes. 2025-06-16 https://github.com/shenwei356/LexicMap 0.9.0 lexicmap 0.9.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lexicmap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lexicmap lexicmap LexicMap LexicMap is a nucleotide sequence alignment tool for efficiently querying gene, plasmid, viral, or long-read sequences (>100 bp) against up to millions of prokaryotic genomes. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +liana liana_methods, liana_misty, liana_multi, liana_plot, liana_resource, liana_utils h5mu, txt, npy, h5ad, png, pdf, svg, tabular LIANA+ - Ligand-receptor analysis framework 2026-03-10 https://liana-py.readthedocs.io 1.7.1 liana 1.7.3 To update Single Cell, Spatial Omics, Transcriptomics Expression profile clustering, Principal component visualisation, Differential gene expression profiling Expression profile clustering, Principal component visualisation, Differential gene expression profiling Single-cell sequencing, Cell biology, Gene expression, Genetics Cell biology, Gene expression, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/liana /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/liana liana Liana+ LIANA+ is a scalable framework for inference of cell‑cell communication (CCC) from single-cell and spatially resolved omics data. It integrates multiple ligand‑receptor inference methods and expert curated resources into a unified pipeline, supports consensus ranking across methods, and facilitates differential and contextual CCC analyses. LIANA+ accepts AnnData/MuData formats and interfaces with single‑cell ecosystems like scverse for flexible, interoperable workflows. 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +liftoff liftoff gff3, txt Lift gene annotations between genome assemblies using Liftoff 2026-02-02 https://github.com/agshumate/Liftoff @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ liftoff 1.6.3 To update Sequence Analysis Genome assembly, Mapping assembly, Mapping Genome assembly, Mapping assembly, Mapping Gene transcripts, Sequence assembly, Mapping, Gene expression, RNA immunoprecipitation Gene transcripts, Sequence assembly, Mapping, Gene expression, RNA immunoprecipitation iuc https://github.com/galaxyproject/tools-iuc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/liftoff liftoff Liftoff An accurate gene annotation mapping tool. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +limma_voom limma_voom html, tabular, txt Perform RNA-Seq differential expression analysis using limma voom pipeline 2017-05-24 http://bioconductor.org/packages/release/bioc/html/limma.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-limma 3.66.0 To update Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Molecular biology, Genetics Molecular biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/limma_voom /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/limma_voom limma limma Data analysis, linear models and differential expression for microarray data. 1 2902 3166 27013 30001 5247 6265 50381 59995 921 1003 10130 11326 26 26 329 329 101651 87853 10460 9096 +lineagespot lineagespot tabular Identification of SARS-CoV-2 related metagenomic mutations based on a single (or a list of) variant(s) file(s) 2023-07-04 https://www.bioconductor.org/packages/release/bioc/html/lineagespot.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-base To update Metagenomics, Sequence Analysis Variant calling Variant calling Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation Metagenomics, Gene transcripts, Evolutionary biology, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lineagespot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lineagespot lineagespot lineagespot Lineagespot is a framework written in R, and aims to identify and assign different SARS-CoV-2 lineages based on a single variant file (i.e., variant calling format). 1 4 4 39 39 0 0 0 0 0 0 0 0 0 0 0 0 39 39 4 4 +links links fasta, tabular, graph_dot Scaffold genome assemblies with long reads. 2022-02-23 https://github.com/bcgsc/LINKS @TOOL_VERSION@+galaxy+@VERSION_SUFFIX@ links 2.0.1 To update Assembly Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Scaffolding, Genome assembly, Read mapping, Read pre-processing, Sequence trimming Sequence assembly, Mapping, Sequencing Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/links /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/links links LINKS LINKS (Long Interval Nucleotide K-mer Scaffolder) is a genomics application for scaffolding genome assemblies with long reads, such as those produced by Oxford Nanopore Technologies Ltd. It can be used to scaffold high-quality draft genome assemblies with any long sequences (eg. ONT reads, PacBio reads, other draft genomes, etc). It is also used to scaffold contig pairs linked by ARCS/ARKS. 1 181 181 940 940 0 0 0 0 87 87 778 778 0 0 0 0 1718 1718 268 268 +lofreq lofreq_alnqual, lofreq_call, lofreq_filter, lofreq_indelqual, lofreq_viterbi bam, vcf LoFreq is a fast and sensitive variant-caller for inferring SNVs and indelsfrom next-generation sequencing data. It makes full use of base-call qualitiesand other sources of errors inherent in sequencing (e.g. mapping or base/indelalignment uncertainty), which are usually ignored by other methods or onlyused for filtering. 2019-11-25 https://csb5.github.io/lofreq/ 2.1.5 lofreq 2.1.5 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lofreq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lofreq 5 2011 2074 3863858 4206633 4705 5024 450169 545066 673 701 127920 138242 52 54 8858 8924 4898865 4450805 7853 7441 +longdust longdust bed Detect low-complexity regions in long DNA sequences using k-mer statistics. 2025-10-01 https://github.com/lh3/longdust 1.4 longdust 1.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/longdust /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/longdust 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +lorikeet_spoligotype lorikeet_spoligotype txt Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 2018-05-07 https://github.com/AbeelLab/lorikeet @TOOL_VERSION@ lorikeet 20 To update Sequence Analysis Sequence analysis, Genotyping Sequence analysis, Genotyping Genotype and phenotype Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lorikeet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lorikeet lorikeet lorikeet Tools for M. tuberculosis DNA fingerprinting (spoligotyping) 1 18 18 930 930 0 0 0 0 0 0 0 0 0 0 0 0 930 930 18 18 +lumpy_sv lumpy_prep, lumpy_sv qname_sorted.bam, bam, vcf LUMPY - a general probabilistic framework for structural variant discovery 2020-11-12 https://github.com/arq5x/lumpy-sv 0.3.1 lumpy-sv 0.3.1 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/lumpy_sv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/lumpy_sv 2 139 139 2586 2586 0 0 0 0 0 0 0 0 0 0 0 0 2586 2586 139 139 +m6anet m6anet tabular m6anet to detect m6A RNA modifications from nanopore data 2023-10-25 https://m6anet.readthedocs.io/en/latest @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ m6anet 2.1.0 To update Sequence Analysis Quantification, Imputation, Gene expression profiling Quantification, Imputation, Gene expression profiling RNA-Seq, Transcriptomics, RNA, Machine learning RNA-Seq, Transcriptomics, RNA, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/m6anet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/m6anet m6Anet m6Anet Detection of m6A from direct RNA sequencing using a Multiple Instance Learning framework. 1 12 12 47 47 0 0 0 0 0 0 0 0 0 0 0 0 47 47 12 12 +maaslin2 maaslin2 zip, tabular, rdata, pdf MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata. 2021-11-05 http://huttenhower.sph.harvard.edu/maaslin 1.18.0 bioconductor-maaslin2 1.18.0 Up-to-date Metagenomics Filtering, Statistical calculation, Standardisation and normalisation, Visualisation Filtering, Standardisation and normalisation, Visualisation Metagenomics, Statistics and probability Metagenomics, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maaslin2 maaslin2 MaAsLin2 MaAsLin2 is comprehensive R package for efficiently determining multivariable association between phenotypes, environments, exposures, covariates and microbial meta’omic features. MaAsLin2 relies on general linear models to accommodate most modern epidemiological study designs, including cross-sectional and longitudinal, and offers a variety of data exploration, normalization, and transformation methods. 1 100 100 3676 3676 0 0 0 0 0 0 0 0 2 2 4 4 3680 3680 102 102 +maaslin3 maaslin3 tabular, png, pdf MaAsLin 3 is the next generation of MaAsLin. This comprehensive R package efficiently determines multivariable associations between clinical metadata and microbial meta-omics features. 2025-11-05 https://github.com/biobakery/maaslin3 0.99.16 maaslin3 0.99.16 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maaslin3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maaslin3 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +macs2 macs2_bdgbroadcall, macs2_bdgcmp, macs2_bdgdiff, macs2_bdgpeakcall, macs2_callpeak, macs2_filterdup, macs2_predictd, macs2_randsample, macs2_refinepeak interval, bedgraph, bed, tabular, pdf, html, txt MACS - Model-based Analysis of ChIP-Seq 2014-11-12 https://github.com/taoliu/MACS 2.2.9.1 macs2 2.2.9.1 Up-to-date Sequence Analysis, Statistics Peak calling, Enrichment analysis, Gene regulatory network analysis Peak calling, Enrichment analysis, Gene regulatory network analysis ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites ChIP-seq, Molecular interactions, pathways and networks, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/macs2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/macs2 macs MACS Model-based Analysis of ChIP-seq data. https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379 9 4539 5553 101779 121444 9434 15168 156715 260074 584 718 11876 14828 423 423 5024 5066 401412 275394 21862 14980 +maf_stats maf_stats1 interval MAF Coverage statistics 2020-08-12 https://github.com/galaxyproject/tools-iuc/tree/master/tools/interval2maf/ 1.0.2 To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maf_stats /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maf_stats 1 5 9 9 21 47 469 176 2482 1 1 1 1 0 0 0 0 2504 186 479 53 +maf_tools ucsc_mafaddirows, ucsc_mafcoverage, ucsc_maffetch, ucsc_mafFilter, ucsc_maffrag, ucsc_maffrags, ucsc_mafgene maf, txt, fasta Utilities for working with MAF (Multiple Alignment Format) files from UCSC 2025-06-03 http://genome.ucsc.edu @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ucsc-mafaddirows 482 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/maftools 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mageck mageck_count, mageck_gsea, mageck_mle, mageck_pathway, mageck_test tabular, pdf, txt Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identifyimportant genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 2017-11-08 https://sourceforge.net/projects/mageck/ 0.5.9.2 mageck 0.5.9.5 To update Genome editing Genetic variation analysis Genetic variation analysis Genetics, Genetic variation, Genomics Genetics, Genetic variation, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mageck /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mageck mageck MAGeCK Computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. 5 407 423 13575 15010 433 433 13443 13443 137 139 6643 7099 5 5 41 41 35593 33702 1000 982 +magicblast magicblast bam Maps large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome 2022-04-05 https://ncbi.github.io/magicblast/ 1.7.0 magicblast 1.7.0 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/blast /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/blast 1 230 230 8803 8803 0 0 0 0 1 1 2 2 0 0 0 0 8805 8805 231 231 +maker maker, maker_map_ids gff3, gff, tabular MAKER is a portable and easily configurable genome annotation pipeline.Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2017-10-04 http://www.yandell-lab.org/software/maker.html 2.31.11 maker 3.01.04 To update Sequence Analysis Genome annotation Genome annotation Genomics, DNA, Sequence analysis Genomics, DNA, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maker /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maker maker MAKER Portable and easily configurable genome annotation pipeline. It’s purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. 2 1323 1455 7332 8835 1701 1808 9536 10359 904 904 4968 4989 33 33 211 211 24394 22047 4200 3961 +malt_run malt_run rma6, sam, fasta Aligns an input sequence (DNA or proteins) against an index representing a collection of reference DNA or protein sequences. 2021-11-12 https://github.com/husonlab/malt 0.5.3 malt 0.62 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/malt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/malt 1 9 9 27 27 0 0 0 0 0 0 0 0 0 0 0 0 27 27 9 9 +map_damage map_damage txt, bam, fasta Tracks and quantifies specific ancient DNA damage patterns for authentication. 2025-06-27 https://ginolhac.github.io/mapDamage/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mapdamage2 2.2.3 To update Sequence Analysis, Statistics, Visualization Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_damage /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/map_damage mapdamage MapDamage Identify and quantify DNA damage patterns in ancient DNA. 1 3 3 36 36 0 0 0 0 0 0 0 0 2 2 3 3 39 39 5 5 +map_param_value map_param_value Map a parameter value to another value 2022-10-13 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/map_param_value /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/map_param_value https://usegalaxy.eu/published/workflow?id=6239178d7cc4ac68, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646 1 163 163 6460 6460 216 216 5530 5530 10 10 321 321 4 4 30 30 12341 12341 393 393 +maplot maplot pdf Generate MA plots for visualizing data distributions using Plotly or Matplotlib. 2025-04-17 https://github.com/galaxyproject/tools-iuc @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plotly To update Visualization, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/maplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maplot 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mapseq mapseq tabular fast and accurate sequence read classification tool designed to assign taxonomy and OTU classifications to ribosomal RNA sequences. 2023-08-02 https://github.com/jfmrod/MAPseq @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ perl To update Metagenomics k-mer counting k-mer counting Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs Functional, regulatory and non-coding RNA, Sequence analysis, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mapseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mapseq mapseq MAPseq Highly efficient k-mer search with confidence estimates, for rRNA sequence analysis . 1 64 64 9612 9612 24 24 434 434 0 0 0 0 0 0 0 0 10046 10046 88 88 +mash mash_dist, mash_paste, mash_screen, mash_sketch tsv, msh, tabular Fast genome and metagenome distance estimation using MinHash 2018-12-07 https://github.com/marbl/Mash 2.3 mash 2.3 Up-to-date Metagenomics Sequence distance matrix generation Sequence distance matrix generation Genomics, Metagenomics, Statistics and probability, Sequence analysis, DNA mutation Metagenomics, Statistics and probability, Sequence analysis, DNA mutation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mash /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mash mash Mash Fast genome and metagenome distance estimation using MinHash. 4 49 57 10768 10867 18 18 922 922 18 18 3187 3187 3 3 29 29 15005 14906 96 88 +mashmap mashmap paf Fast local alignment boundaries 2024-02-26 https://github.com/galaxyproject/tools-iuc/tree/master/tools/mashmap @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mashmap 3.1.3 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mashmap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mashmap 1 33 33 1329 1329 35 35 1094 1094 0 0 0 0 0 0 0 0 2423 2423 68 68 +masigpro masigpro txt, pdf, tabular Identify significantly differential expression profiles in time-course microarray experiments 2017-05-09 https://www.bioconductor.org/packages/release/bioc/html/maSigPro.html @TOOL_VERSION@.1+galaxy@VERSION_SUFFIX@ coreutils 8.25 To update Transcriptomics, RNA, Statistics Regression analysis Regression analysis Gene expression, Molecular genetics, Microarray experiment, RNA-Seq Gene expression, Microarray experiment, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/masigpro /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/masigpro masigpro maSigPro Regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments. 1 35 44 200 628 75 88 522 630 0 0 0 0 0 0 0 0 1258 722 132 110 +maxbin2 maxbin2 fasta, tabular, txt, pdf clusters metagenomic contigs into bins 2019-10-24 https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html @MAXBIN_VERSION@ maxbin2 2.2.7 To update Metagenomics Sequence assembly Sequence assembly Metagenomics, Sequence assembly, Microbiology Metagenomics, Sequence assembly, Microbiology mbernt https://github.com/galaxyproject/tools-iuc/tree/main/tools/maxbin2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/maxbin2 maxbin MaxBin Software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. 1 408 433 5244 5537 634 675 2694 2993 106 108 1135 1198 6 6 648 648 10376 9721 1222 1154 +mcl mcl tabular The Markov Cluster Algorithm, a cluster algorithm for graphs 2022-05-12 https://micans.org/mcl/man/mcl.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mcl 22.282 To update Sequence Analysis Clustering, Network analysis, Gene regulatory network analysis Clustering, Gene regulatory network analysis Molecular interactions, pathways and networks Molecular interactions, pathways and networks iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mcl /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mcl mcl MCL MCL is a clustering algorithm widely used in bioinformatics and gaining traction in other fields. 1 18 18 153 153 0 0 0 0 0 0 0 0 0 0 0 0 153 153 18 18 +medaka medaka_consensus, medaka_consensus_pipeline, medaka_variant h5, txt, fasta, bam, bed, vcf, tabular Sequence correction provided by ONT Research 2020-02-23 https://github.com/nanoporetech/medaka 2.1.1 medaka 2.2.2 To update Sequence Analysis Base-calling, Variant calling, Sequence assembly Base-calling, Variant calling, Sequence assembly Sequence assembly, Machine learning Sequence assembly, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/medaka /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/medaka medaka Medaka medaka is a tool to create consensus sequences and variant calls from nanopore sequencing data. This task is performed using neural networks applied a pileup of individual sequencing reads against a draft assembly. microbiome/pathogen-detection-from-nanopore-foodborne-data 3 1728 1734 155538 156220 735 735 76698 76698 421 421 11622 11622 17 17 2659 2659 247199 246517 2907 2901 +megahit megahit fasta, txt An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. 2017-09-22 https://github.com/voutcn/megahit @TOOL_VERSION@ megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/megahit megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. microbiome/metagenomics-assembly, microbiome/metagenomics-binning 1 2052 2197 22340 24371 2823 2929 23973 24874 615 632 9338 9643 54 54 1387 1387 60275 57038 5812 5544 +megahit_contig2fastg megahit_contig2fastg fastg A subprogram within the Megahit toolkit for converting contigs to assembly graphs (fastg) 2018-11-08 https://github.com/voutcn/megahit/blob/master/tools/toolkit.cpp @VERSION@+@GALAXY_VERSION@ megahit 1.2.9 To update Sequence Analysis, Assembly, Metagenomics Genome assembly Genome assembly Metagenomics, Sequencing, Ecology, Sequence assembly Metagenomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megahit_contig2fastg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/megahit_contig2fastg megahit MEGAHIT Single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph to achieve low memory usage, whereas its goal is not to make memory usage as low as possible. microbiome/metagenomics-assembly 1 200 212 763 862 113 113 338 338 33 33 150 150 6 6 80 80 1430 1331 364 352 +megan megan_blast2lca, megan_blast2rma, megan_daa2info, megan_daa2rma, megan_daa_meganizer, megan_read_extractor, megan_sam2rma txt, rma6, daa MEGAN Community Edition - Interactive exploration and analysis of large-scale microbiome sequencing data. MEGAN is a tool for studying the taxonomic content of a set of DNA reads, typically collected in a metagenomics project.In a preprocessing step, a sequence alignment of all reads against a suitable database of reference DNA or proteinsequences must be performed to produce an input file for the program. MEGAN is suitable for DNA reads (metagenomedata), RNA reads (metatranscriptome data), peptide sequences (metaproteomics data) and, using a suitable synonymsfile that maps SILVA ids to taxon ids, for 16S rRNA data (amplicon sequencing). 2021-11-24 https://github.com/husonlab/megan-ce 6.21.7 megan 6.25.10 To update Sequence Analysis Sequence analysis, Taxonomic classification Sequence analysis, Taxonomic classification Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/megan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/megan megan MEGAN Metagenome Analysis Software - MEGAN (MEtaGenome ANalyzer) is a new computer program that allows laptop analysis of large metagenomic datasets. In a preprocessing step, the set of DNA reads (or contigs) is compared against databases of known sequences using BLAST or another comparison tool. MEGAN can then be used to compute and interactively explore the taxonomical content of the dataset, employing the NCBI taxonomy to summarize and order the results. 7 250 250 5164 5164 0 0 0 0 5 5 72 72 3 3 4 4 5240 5240 258 258 +meme meme_dreme, meme_fimo, meme_meme, meme_psp_gen, meme_streme html, txt, memexml, gff, memepsp, tabular The MEME Suite allows the biologist to discover novel motifs in collections of unaligned nucleotideor protein sequences, and to perform a wide variety of other motif-based analyses. 2015-12-13 http://meme-suite.org/ 5.5.8 meme 5.5.9 To update ChIP-seq Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction Sequence motif discovery, Sequence motif recognition, Sequence motif comparison, Transcriptional regulatory element prediction Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules Sequence sites, features and motifs, ChIP-seq, RNA immunoprecipitation, Epigenetics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/meme streme STREME STREME is accurate and versatile sequence motif discovery tool. The MEME Suite allows you to discover novel motifs in collections of unaligned nucleotide or protein sequences, and to perform a wide variety of other motif-based analyses. It provides motif discovery algorithms using both probabilistic (MEME) and discrete models (STREME), which have complementary strengths. It also allows discovery of motifs with arbitrary insertions and deletions (GLAM2). MEME-ChIP performs a comprehensive motif-based analysis of ChIP-seq and other large sequence datasets. 5 476 632 6756 24611 1135 2866 9050 27707 0 0 0 0 0 2 0 150 52468 15806 3500 1611 +meme_chip meme_chip html Performs motif discovery, motif enrichment analysis and clustering on large nucleotide datasets. 2018-03-15 http://meme-suite.org/ 4.11.2 graphicsmagick 1.3.26 To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meme_chip /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/meme_chip 1 724 899 6897 8466 1240 1394 7722 8507 0 0 0 0 0 0 0 0 16973 14619 2293 1964 +meningotype meningotype tabular Assign sequence type to N. meningitidis genome assemblies 2023-06-06 https://github.com/MDU-PHL/meningotype @TOOL_VERSION@ meningotype 0.8.6b To update Sequence Analysis Genotyping, Multilocus sequence typing Multilocus sequence typing Microbiology, Genotype and phenotype Microbiology, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meningotype /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/meningotype meningotype meningotype In silico typing of Neisseria meningitidis contigs. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +merlin merlin txt Pedigree Analysis package 2020-04-15 http://csg.sph.umich.edu/abecasis/Merlin/ @TOOL_VERSION@.3 merlin 1.1.2 To update Variant Analysis Haplotype mapping, Genetic mapping Haplotype mapping GWAS study, Mapping GWAS study, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merlin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/merlin merlin Merlin Can be used for parametric and non-parametric linkage analysis, regression-based linkage analysis or association analysis for quantitative traits, ibd and kinship estimation, haplotyping, error detection and simulation 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +merqury merqury, merquryplot txt Merqury is a tool for evaluating genomes assemblies based of k-mer operations. 2021-04-19 https://github.com/marbl/merqury 1.3 merqury 1.3 Up-to-date Assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Genome assembly, k-mer counting, Scaffolding, Phasing, De-novo assembly Sequence assembly, Whole genome sequencing, Plant biology Sequence assembly, Whole genome sequencing, Plant biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merqury /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/merqury merqury Merqury Reference-free quality, completeness, and phasing assessment for genome assemblies.Evaluate genome assemblies with k-mers and more.Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual.Merqury provides a set of tools for this purpose. https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/403?version=9, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 2 661 661 4657 4657 264 264 1645 1645 243 243 1945 1945 77 77 440 440 8687 8687 1245 1245 +merquryfk merquryfk_asmplot, merquryfk_cnplot, merquryfk_hapmaker, merquryfk_happlot, merquryfk_merquryfk fastk_ktab, fastk_ktab_tar, png, pdf, tabular, bed FastK based version of Merqury 2025-02-11 https://github.com/thegenemyers/MERQURY.FK 1.1.1 merquryfk 1.2 To update Sequence Analysis, Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/merquryfk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/merquryfk 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +meryl meryl_arithmetic_kmers, meryl_count_kmers, meryl_filter_kmers, meryl_groups_kmers, meryl_histogram_kmers, meryl_print, meryl_trio_mode meryldb, tabular Meryl a k-mer counter. 2021-04-05 https://github.com/marbl/meryl 1.4.1 merqury 1.3 To update Assembly k-mer counting k-mer counting Whole genome sequencing, Genomics, Sequence analysis, Sequencing Whole genome sequencing, Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/meryl /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/meryl meryl Meryl Meryl is a tool for counting and working with sets of k-mers that was originally developed for use in the Celera Assembler and has since been migrated and maintained as part of Canu. 7 55 55 1850 1850 77 77 1478 1478 0 0 0 0 0 0 0 0 3328 3328 132 132 +metabat2 metabat2_jgi_summarize_bam_contig_depths, metabat2 tabular, fasta, txt MetaBAT2 (Metagenome Binning based on Abundance and Tetranucleotide frequency) is an automated metagenome binningsoftware that integrates empirical probabilistic distances of genome abundance and tetranucleotide frequency. 2022-01-28 https://bitbucket.org/berkeleylab/metabat/src/master/ 2.18.23 metabat2 2.18_23_gc869c52 To update Metagenomics Read binning, Sequence assembly, Genome annotation Read binning, Sequence assembly, Genome annotation Metagenomics, Sequence assembly, Metagenomic sequencing Metagenomics, Sequence assembly, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabat2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metabat2 MetaBAT_2 MetaBAT 2 "an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies | MetaBAT2 clusters metagenomic contigs into different ""bins"", each of which should correspond to a putative genome | MetaBAT2 uses nucleotide composition information and source strain abundance (measured by depth-of-coverage by aligning the reads to the contigs) to perform binning" 2 670 670 14194 14194 375 375 2591 2591 167 167 1738 1738 18 18 1359 1359 19882 19882 1230 1230 +metabuli metabuli_classify tabular, html, txt Classifying metagenomes by jointly analysing both DNA and amino acid (AA) sequences 2024-06-04 https://github.com/steineggerlab/Metabuli 1.0.5 metabuli 1.2.0 To update Sequence Analysis, Metagenomics Taxonomic classification Taxonomic classification Taxonomy Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metabuli /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metabuli metabuli metabuli Metabuli: specific and sensitive metagenomic classification via joint analysis of DNA and amino acid 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +metaeuk metaeuk_easy_predict fasta, gff MetaEuk is a modular toolkit designed for large-scale gene discovery andannotation in eukaryotic metagenomic contigs. Metaeuk combines the fast andsensitive homology search capabilities of MMseqs2 with a dynamic programmingprocedure to recover optimal exons sets. It reduces redundancies in multiplediscoveries of the same gene and resolves conflicting gene predictions onthe same strand. 2020-08-04 https://github.com/soedinglab/metaeuk @TOOL_VERSION@ metaeuk 6.a5d39d9 To update Sequence Analysis, Genome annotation Homology-based gene prediction Homology-based gene prediction Metagenomics, Gene and protein families Metagenomics, Gene and protein families iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaeuk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metaeuk MetaEuk MetaEuk MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics 1 57 58 507 509 0 0 0 0 0 0 0 0 0 0 0 0 509 507 58 57 +metagenomeseq_normalization metagenomeseq_normalizaton tabular, txt metagenomeSeq Normalization 2017-03-27 https://bioconductor.org/packages/3.18/bioc/html/metagenomeSeq.html 1.16.0-0.0.1 bioconductor-metagenomeseq 1.52.0 To update Metagenomics Sequence visualisation, Statistical calculation Sequence visualisation, Statistical calculation Metagenomics, Sequencing Metagenomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metagenomeseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metagenomeseq metagenomeseq metagenomeSeq Designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. It is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations. 1 15 23 521 763 28 56 261 530 0 0 0 0 0 0 0 0 1293 782 79 43 +metamdbg metamdbg_asm, metamdbg_gfa fasta.gz, tar.gz, txt, gfa1 MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads. 2025-02-04 https://github.com/GaetanBenoitDev/metaMDBG 1.4 metamdbg 1.4 Up-to-date Assembly, Metagenomics Genome assembly Genome assembly Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metamdbg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metamdbg metamdbg metaMDBG MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi, Nanopore r10.4). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly. MetaMDBG combines an efficient multi-k approach in minimizer-space for dealing with uneven species coverages, and a novel abundance-based filtering method for simplifying strain complexity. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +metaphlan customize_metaphlan_database, extract_metaphlan_database, merge_metaphlan_tables, metaphlan fasta, json, tabular, sam, biom1, fastqsanger MetaPhlAn for Metagenomic Phylogenetic Analysis 2021-03-11 https://github.com/biobakery/MetaPhlAn 4.2.4 metaphlan 4.2.4 Up-to-date Metagenomics Taxonomic classification, Taxonomic classification Taxonomic classification, Taxonomic classification Metagenomics, Phylogenomics Metagenomics, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metaphlan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metaphlan metaphlan MetaPhlAn Computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. https://usegalaxy.eu/published/workflow?id=b14845359b702444 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/taxonomic-profiling 4 1552 1552 30934 31014 1122 1122 20021 20021 314 314 6347 6347 28 28 211 211 57593 57513 3016 3016 +metasbt metasbt_index, metasbt_profile tabular, tar Microbial genomes characterization with Sequence Bloom Trees 2025-08-22 https://github.com/cumbof/MetaSBT 0.1.5 sed To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/metasbt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metasbt 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +metawrapmg_binning metawrapmg_binning, metawrapmg_bin_refinement A flexible pipeline for genome-resolved metagenomic data analysis 2024-04-12 https://github.com/bxlab/metaWRAP 1.3.0 metawrap-mg 1.3.0 Up-to-date Metagenomics Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Read binning, Sequence assembly, Genome annotation, Sequence trimming, Demultiplexing Whole genome sequencing, Metagenomic sequencing, Metagenomics Whole genome sequencing, Metagenomic sequencing, Metagenomics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/metawrapmg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/metawrapmg metawrap MetaWRAP MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. 2 100 100 1596 1596 0 0 0 0 67 67 587 587 0 0 0 0 2183 2183 167 167 +mg_toolkit mg_toolkit_bulk_download, mg_toolkit_original_metadata tsv Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2024-07-12 https://github.com/EBI-Metagenomics/emg-toolkit 0.10.4 mg-toolkit 0.10.4 Up-to-date Metagenomics Data retrieval Data retrieval Metagenomics Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mg_toolkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mg_toolkit mg-toolkit mg-toolkit Metagenomics toolkit enables scientists to download all of the sample metadata for a given study or sequence to a single csv file. 2 10 10 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 10 10 +mgnify_genome_search mgnify_genome_search tabular Queue genomes against registered genome from MGnify Database 2026-01-26 https://github.com/SantaMcCloud/MGnify-genome-search @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mgnify-genome-search 1.0.0 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_genome_search /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mgnify_genome_search 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mgnify_pipelines_toolkit mgnify_pipelines_toolkit_classify_var_regions, mgnify_pipelines_toolkit_make_asv_count_table, mgnify_pipelines_toolkit_mapseq_to_asv_table, mgnify_pipelines_toolkit_permute_primers, mgnify_pipelines_toolkit_primer_val_classification, mgnify_pipelines_toolkit_rev_comp_se_primers json, tabular, txt, tsv, fasta Utilities for use in the MGnify pipelines 2026-04-22 https://github.com/EBI-Metagenomics/mgnify-pipelines-toolkit 1.5.1 mgnify-pipelines-toolkit 1.5.1 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mgnify_pipelines_toolkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mgnify_pipelines_toolkit 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +micro_decon micro_decon csv An R package for removing contamination from metabarcoding (e.g., microbiome) datasets post-sequencing 2025-08-05 https://github.com/donaldtmcknight/microdecon 1.0.2 To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/micro_decon /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/micro_decon 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +microsatbed microsatbed bed Select microsatellites for a bed file 2024-07-21 https://github.com/lmdu/pytrf @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/microsatbed /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/microsatbed 1 16 16 949 949 20 20 740 740 0 0 0 0 0 0 0 0 1689 1689 36 36 +migmap migmap tabular mapper for full-length T- and B-cell repertoire sequencing 2017-09-28 https://github.com/mikessh/migmap @TOOL_VERSION@ migmap 1.0.3 To update RNA, Sequence Analysis Sequence analysis, Read mapping Sequence analysis, Read mapping Immunoproteins, genes and antigens, Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/migmap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/migmap MiGMAP MiGMAP Mapper for full-length T- and B-cell repertoire sequencing. 1 24 39 931 1301 73 101 1138 1564 0 0 0 0 0 0 0 0 2865 2069 140 97 +minia minia fasta Short-read assembler based on a de Bruijn graph 2020-04-08 https://gatb.inria.fr/software/minia/ @TOOL_VERSION@ minia 3.2.6 To update Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minia /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/minia minia Minia Short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. 1 272 287 6758 7224 0 0 0 0 77 77 357 357 0 0 0 0 7581 7115 364 349 +miniasm miniasm tabular Miniasm - Ultrafast de novo assembly for long noisy reads (though having no consensus step) 2019-06-18 https://github.com/lh3/miniasm @TOOL_VERSION@ miniasm 0.3 To update Assembly De-novo assembly De-novo assembly Genomics, Sequence assembly Genomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniasm /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/miniasm miniasm miniasm Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. microbiome/plasmid-metagenomics-nanopore 1 571 687 11506 14702 474 538 9124 10016 88 96 1235 1277 16 16 166 166 26161 22031 1337 1149 +minimap2 minimap2 bam A fast pairwise aligner for genomic and spliced nucleotide sequences 2017-11-03 https://github.com/lh3/minimap2 2.31 minimap2 2.31 Up-to-date Next Gen Mappers Pairwise sequence alignment Pairwise sequence alignment Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/minimap2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/minimap2 minimap2 Minimap2 Pairwise aligner for genomic and spliced nucleotide sequences https://workflowhub.eu/workflows/1104?version=2 microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore 1 5844 6182 414670 442793 5535 5834 153408 159247 1454 1492 29827 30676 169 170 4829 4841 637557 602734 13678 13002 +miniprot miniprot, miniprot_index gff3, binary Align a protein sequence against a genome with affine gap penalty, splicing and frameshift. 2022-09-19 https://github.com/lh3/miniprot 0.18 miniprot 0.18 Up-to-date Sequence Analysis Sequence alignment, Protein sequence analysis Sequence alignment, Protein sequence analysis Sequence sites, features and motifs, Sequence analysis Sequence sites, features and motifs, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/miniprot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/miniprot miniprot miniprot Miniprot aligns a protein sequence against a genome with affine gap penalty, splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 2 100 100 5038 5038 42 42 364 364 0 0 0 0 25 25 283 283 5685 5685 167 167 +mirmachine mirmachine gff, fasta Tool to detect miRNA in genome sequences 2024-03-15 https://github.com/sinanugur/MirMachine 0.3.0.4 mirmachine 0.3.0.4 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirmachine /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mirmachine 1 10 10 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 10 10 +mirnature mirnature txt Computational detection of canonical microRNAs 2022-12-11 https://github.com/Bierinformatik/miRNAture 1.1 mirnature 1.1 Up-to-date RNA, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mirnature /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mirnature 1 11 11 23 23 0 0 0 0 0 0 0 0 0 0 0 0 23 23 11 11 +mist_typing mist_call, mist_dists tabular, json Wrappers for Minimap2-inferred Sequence Typing (MiST). 2026-01-08 https://github.com/BioinformaticsPlatformWIV-ISP/MiST 1.2.0 mist_typing 1.2.0 Up-to-date Sequence Analysis, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mist_typing /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mist_typing 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mitobim mitobim fasta assemble mitochondrial genomes 2020-12-29 https://github.com/chrishah/MITObim @TOOL_VERSION@+galaxy@GALAXY_VERSION@ mitobim 1.9.1 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitobim /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mitobim 1 168 168 1463 1463 0 0 0 0 39 39 533 533 0 0 0 0 1996 1996 207 207 +mitos mitos, mitos2 bed, tabular, gff, txt, fasta, pdf, zip de-novo annotation of metazoan mitochondrial genomes 2020-02-18 http://mitos.bioinf.uni-leipzig.de/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mitos 2.1.10 To update Sequence Analysis Genome annotation Genome annotation Zoology, Whole genome sequencing Zoology, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mitos /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mitos mitos MITOS De novo metazoan mitochondrial genome annotation. 2 1326 1336 267673 268177 772 772 84561 84561 151 151 15492 15492 6 6 109 109 368339 367835 2265 2255 +mlst mlst, mlst_list tabular, fasta, txt Scan contig files against PubMLST typing schemes 2016-12-13 https://github.com/tseemann/mlst 2.22.0 mlst 2.35.0 To update Sequence Analysis Multilocus sequence typing Multilocus sequence typing Immunoproteins and antigens Immunoproteins and antigens iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mlst /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mlst mlst MLST Multi Locus Sequence Typing from an assembled genome or from a set of reads. microbiome/pathogen-detection-from-nanopore-foodborne-data 2 1786 1918 24365 26341 1356 1420 12903 13604 1137 1439 12595 15564 22 22 99 99 55608 49962 4799 4301 +mmseqs2 mmseqs2_easy_cluster, mmseqs2_easy_linclust_clustering, mmseqs2_easy_linsearch, mmseqs2_easy_rbh, mmseqs2_easy_search, mmseqs2_easy_taxonomy, mmseqs2_taxonomy_assignment tabular, txt, html MMseqs2 is an ultra fast and sensitive sequence search and clustering suite 2025-03-27 https://github.com/soedinglab/MMseqs2 17-b804f mmseqs2 17.b804f To update Sequence Analysis, Metagenomics Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Sequence similarity search, Sequence alignment, Sequence clustering, Taxonomic classification Metagenomics, Sequence analysis, Proteins, Nucleic acids, Gene and protein families, Taxonomy Metagenomics, Sequence analysis, Nucleic acids, Gene and protein families, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmseqs2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mmseqs2 MMseqs2 MMseqs2 MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. MMseqs2 is open source software implemented in C++ for Linux, MacOS, and (as beta version, via cygwin) Windows. The software is designed to run on multiple cores and servers and exhibits very good scalability. MMseqs2 can run 10000 times faster than BLAST. At 100 times its speed it achieves almost the same sensitivity. It can perform profile searches with the same sensitivity as PSI-BLAST at over 400 times its speed.MMseqs2 includes Linclust, the first clustering algorithm whose runtime scales linearly With Linclust we clustered 1.6 billion metagenomic sequence fragments in 10 h on a single server to 50% sequence identity. 7 42 42 260 260 0 0 0 0 0 0 0 0 3 3 29 29 289 289 45 45 +mmuphin mmuphin tabular, pdf MMUPHin is an R package implementing meta-analysis methods for microbial community profiles 2024-11-22 https://huttenhower.sph.harvard.edu/mmuphin 1.16.0 bioconductor-mmuphin 1.16.0 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mmuphin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mmuphin mmuphin mmuphin MMUPHin is an R package for meta-analysis tasks of microbiome cohorts. It has function interfaces for: a) covariate-controlled batch- and cohort effect adjustment, b) meta-analysis differential abundance testing, c) meta-analysis unsupervised discrete structure (clustering) discovery, and d) meta-analysis unsupervised continuous structure discovery. 1 3 3 14 14 0 0 0 0 0 0 0 0 0 0 0 0 14 14 3 3 +moabs moabs interval MOABS for differential methylation analysis on Bisulfite sequencing data. 2019-07-27 https://github.com/sunnyisgalaxy/moabs 1.3.4.6 moabs 1.3.9.6 To update Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/moabs /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/moabs 1 46 59 185 351 0 0 0 0 0 0 0 0 0 0 0 0 351 185 59 46 +mosdepth mosdepth tabular, bedgraph, bed fast and flexible BAM/CRAM depth calculation 2022-12-04 https://github.com/brentp/mosdepth @TOOL_VERSION@ mosdepth 0.3.14 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mosdepth /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mosdepth 1 201 201 14592 14592 173 173 13590 13590 73 73 3292 3292 1 1 1500 1500 32974 32974 448 448 +mothur mothur_align_check, mothur_align_seqs, mothur_amova, mothur_anosim, mothur_bin_seqs, mothur_biom_info, mothur_chimera_bellerophon, mothur_chimera_ccode, mothur_chimera_check, mothur_chimera_perseus, mothur_chimera_pintail, mothur_chimera_slayer, mothur_chimera_uchime, mothur_chimera_vsearch, mothur_chop_seqs, mothur_classify_otu, mothur_classify_seqs, mothur_classify_tree, mothur_clearcut, mothur_cluster_classic, mothur_cluster_fragments, mothur_cluster_split, mothur_cluster, mothur_collect_shared, mothur_collect_single, mothur_consensus_seqs, mothur_cooccurrence, mothur_corr_axes, mothur_count_groups, mothur_count_seqs, mothur_create_database, mothur_degap_seqs, mothur_deunique_seqs, mothur_deunique_tree, mothur_dist_seqs, mothur_dist_shared, mothur_fastq_info, mothur_filter_seqs, mothur_filter_shared, mothur_get_communitytype, mothur_get_coremicrobiome, mothur_get_dists, mothur_get_group, mothur_get_groups, mothur_get_label, mothur_get_lineage, mothur_get_mimarkspackage, mothur_get_otulabels, mothur_get_otulist, mothur_get_oturep, mothur_get_otus, mothur_get_rabund, mothur_get_relabund, mothur_get_sabund, mothur_get_seqs, mothur_get_sharedseqs, mothur_heatmap_bin, mothur_heatmap_sim, mothur_homova, mothur_indicator, mothur_lefse, mothur_libshuff, mothur_list_otulabels, mothur_list_seqs, mothur_make_biom, mothur_make_contigs, mothur_make_design, mothur_make_fastq, mothur_make_group, mothur_make_lefse, mothur_make_lookup, mothur_make_shared, mothur_make_sra, mothur_mantel, mothur_merge_count, mothur_merge_files, mothur_merge_groups, mothur_merge_sfffiles, mothur_merge_taxsummary, mothur_metastats, mothur_mimarks_attributes, mothur_nmds, mothur_normalize_shared, mothur_otu_association, mothur_otu_hierarchy, mothur_pairwise_seqs, mothur_parse_list, mothur_parsimony, mothur_pca, mothur_pcoa, mothur_pcr_seqs, mothur_phylo_diversity, mothur_phylotype, mothur_pre_cluster, mothur_primer_design, mothur_rarefaction_shared, mothur_rarefaction_single, mothur_remove_dists, mothur_remove_groups, mothur_remove_lineage, mothur_remove_otulabels, mothur_remove_otus, mothur_remove_rare, mothur_remove_seqs, mothur_rename_seqs, mothur_reverse_seqs, mothur_screen_seqs, mothur_sens_spec, mothur_seq_error, mothur_sffinfo, mothur_shhh_flows, mothur_shhh_seqs, mothur_sort_seqs, mothur_split_abund, mothur_split_groups, mothur_sub_sample, mothur_summary_qual, mothur_summary_seqs, mothur_summary_shared, mothur_summary_single, mothur_summary_tax, mothur_taxonomy_to_krona, mothur_tree_shared, mothur_trim_flows, mothur_trim_seqs, mothur_unifrac_unweighted, mothur_unifrac_weighted, mothur_unique_seqs, mothur_venn mothur.align.check, mothur.align, mothur.align.report, mothur.accnos, tabular, mothur.shared, mothur.cons.taxonomy, mothur.tax.summary, txt, mothur.freq, mothur.quan, mothur.count_table, mothur.seq.taxonomy, mothur.tre, mothur.lower.dist, mothur.rabund, mothur.sabund, mothur.list, mothur.names, mothur.axes, mothur.groups, mothur.pair.dist, fasta, qual454, fastq, mothur.filter, mothur.design, mothur.otu.corr, mothur.relabund, svg, qual, mothur.sff.flow, sff, xml, mothur.summary Mothur wrappers 2016-06-24 https://www.mothur.org @WRAPPER_VERSION@.0 mothur 1.48.5 To update Metagenomics DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis DNA barcoding, Sequencing quality control, Sequence clustering, Taxonomic classification, Visualisation, Sequence read processing, Phylogenetic analysis Microbial ecology, Taxonomy, Sequence analysis, Phylogeny Microbial ecology, Taxonomy, Sequence analysis, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mothur /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mothur mothur mothur Open-source, platform-independent, community-supported software for describing and comparing microbial communities microbiome/general-tutorial, microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short 129 2291 2805 265024 361038 4027 5455 423935 750968 1447 1742 164152 213607 147 149 14583 14948 1340561 867694 10151 7912 +msaboot msaboot phylip, txt A multiple sequences alignment bootstrapping tool. 2018-02-12 https://github.com/phac-nml/msaboot @VERSION@ msaboot 0.1.2 To update Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/msaboot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/msaboot 1 109 131 1009 1133 199 228 1049 1320 0 0 0 0 0 0 0 0 2453 2058 359 308 +mtnucratio mtnucratio txt, json Calculates Mitochondrial to Nuclear read ratio 2026-03-18 https://github.com/TCLamnidis/mtnucratio @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mtnucratio 0.7.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mtnucratio /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mtnucratio 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +multigps multigps tabular, bed, html Analyzes collections of multi-condition ChIP-seq data. 2017-03-06 http://mahonylab.org/software/multigps/ 0.74.0 fonts-conda-ecosystem To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigps /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/multigps 1 1 1 1 1 121 304 317 891 0 0 0 0 0 0 0 0 892 318 305 122 +multigsea multigsea tabular GSEA-based pathway enrichment analysis for multi-omics data 2023-06-07 https://bioconductor.org/packages/devel/bioc/html/multiGSEA.html 1.12.0 bioconductor-multigsea 1.20.0 To update Transcriptomics, Proteomics, Statistics, Single Cell Gene-set enrichment analysis, Aggregation, Pathway analysis Gene-set enrichment analysis, Aggregation, Pathway analysis Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules Metabolomics, Molecular interactions, pathways and networks, Proteomics, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multigsea /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/multigsea multiGSEA multiGSEA A GSEA-based pathway enrichment analysis for multi-omics data.multiGSEA: a GSEA-based pathway enrichment analysis for multi-omics data, BMC Bioinformatics 21, 561 (2020).Combining GSEA-based pathway enrichment with multi omics data integration. 1 65 65 212 212 0 0 0 0 5 5 46 46 0 0 0 0 258 258 70 70 +multiqc multiqc html, tabular MultiQC aggregates results from bioinformatics analyses across many samples into a single report 2017-09-21 http://multiqc.info/ 1.35 multiqc 1.35 Up-to-date Fastq Manipulation, Statistics, Visualization Validation, Sequencing quality control Sequencing quality control Sequencing, Bioinformatics, Sequence analysis, Genomics Sequencing, Bioinformatics, Sequence analysis, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/multiqc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/multiqc multiqc MultiQC MultiQC aggregates results from multiple bioinformatics analyses across many samples into a single report. It searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792, https://usegalaxy.eu/published/workflow?id=1fe02012c96b731f, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379, https://usegalaxy.eu/published/workflow?id=63478edcea3f449a, https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2, https://usegalaxy.eu/published/workflow?id=deec04097a871646, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 24162 26916 223019 248625 32289 38522 203104 241071 7040 7764 49577 54957 2276 2280 43768 43966 588619 519468 75482 65767 +mummer4 mummer_delta_filter, mummer_dnadiff, mummer_mummer, mummer_mummerplot, mummer_nucmer, mummer_show_coords tabular, txt, png, bam Mummer4 Tools 2018-06-28 https://github.com/mummer4/mummer 4.0.1 mummer4 4.0.1 Up-to-date Sequence Analysis Multiple sequence alignment Multiple sequence alignment Sequence analysis, Human genetics Sequence analysis, Human genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mummer4 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mummer4 mummer4 MUMmer4 System for rapidly aligning large DNA sequences to one another. 6 842 940 30656 33196 1586 1727 32334 36481 295 295 12782 12782 21 21 595 595 83054 76367 2983 2744 +muon cluster_analyze_embed_muon, mudata_import_export, plot_muon, preprocess_muon h5ad, png, pdf, svg, txt muon is a Python framework for multimodal omics analysis 2024-03-15 https://muon.readthedocs.io 0.1.7 muon To update Single Cell, Sequence Analysis, Transcriptomics, Epigenetics Cell biology, Single-cell sequencing, Gene expression, Epigenetics, Multiomics Cell biology, Gene expression, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/muon /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/muon muon muon muon is a Python framework for multimodal omics analysis. 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mykrobe mykrobe_predict csv Antibiotic resistance predictions 2017-12-18 https://github.com/Mykrobe-tools/mykrobe 0.10.0 mykrobe 0.13.0 To update Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Antimicrobial resistance prediction, Variant calling, Genotyping, Sequence trimming Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Probes and primers, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mykrobe /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mykrobe Mykrobe Mykrobe Antibiotic resistance prediction for Mycobacterium tuberculosis from genome sequence data with Mykrobe.Antibiotic resistance prediction in minutes.Table of Contents generated with DocToc.AMR prediction (Mykrobe predictor).Before attempting to install with bioconda, please ensure you have your channels set up as specified in the documentation. If you don't, you may run into issues with an older version of mykrobe being installed 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +mzmine_batch mzmine_batch mass-spectrometry data processing, with the main focus on LC-MS data 2023-10-21 http://mzmine.github.io/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ mzmine 4.7.29 To update Metabolomics Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Natural product identification, Standardisation and normalisation, Peptide database search, Deisotoping, Clustering, Filtering, Chromatographic alignment, Peak detection, Peptide identification, Chromatogram visualisation, Mass spectrum visualisation, Structure visualisation, Plotting, Heat map generation Proteomics, Metabolomics, Proteomics experiment, Small molecules Proteomics, Metabolomics, Proteomics experiment, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/mzmine /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/mzmine mzmine MZmine Toolbox for visualization and analysis of LC-MS data in netCDF or mzXML. 1 8 8 21 21 0 0 0 0 0 0 0 0 0 0 0 0 21 21 8 8 +naltorfs bicodon_counts_from_fasta, codon_freq_from_bicodons, find_nested_alt_orfs tabular, txt, bed, fasta nAlt-ORFs: Nested Alternate Open Reading Frames (nAltORFs) 2022-04-11 https://github.com/BlankenbergLab/nAltORFs 0.1.2 naltorfs 0.1.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/naltorfs /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/naltorfs 3 0 0 0 0 60 60 271 271 0 0 0 0 0 0 0 0 271 271 60 60 +nanocomp nanocomp txt, html Compare multiple runs of long read sequencing data and alignments 2025-05-21 https://github.com/wdecoster/NanoComp @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ nanocomp 1.25.6 To update Visualization, Statistics, Fastq Manipulation Box-Whisker plot plotting, Visualisation, Multiple sample visualisation Box-Whisker plot plotting, Multiple sample visualisation Nucleic acids, Bioinformatics Nucleic acids, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocomp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nanocomp nanocomp nanocomp Compare multiple runs of long read sequencing data and alignments. Creates violin plots or box plots of length, quality and percent identity and creates dynamic, overlaying read length histograms and a cumulative yield plot. 1 2 2 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 2 2 +nanocompore nanocompore_db, nanocompore_sampcomp tabular, tar, txt Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro. 2020-04-28 https://nanocompore.rna.rocks/ 1.0.0rc3.post2 nanocompore 1.0.4 To update Sequence Analysis Post-translation modification site prediction, PolyA signal detection, Genotyping, k-mer counting PolyA signal detection, Genotyping, k-mer counting Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites Functional, regulatory and non-coding RNA, RNA-Seq, Gene transcripts, Transcriptomics, Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanocompore /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nanocompore Nanocompore Nanocompore RNA modifications detection by comparative Nanopore direct RNA sequencing.RNA modifications detection from Nanopore dRNA-Seq data.Nanocompore identifies differences in ONT nanopore sequencing raw signal corresponding to RNA modifications by comparing 2 samples.Analyses performed for the nanocompore paper.Nanocompore compares 2 ONT nanopore direct RNA sequencing datasets from different experimental conditions expected to have a significant impact on RNA modifications. It is recommended to have at least 2 replicates per condition. For example one can use a control condition with a significantly reduced number of modifications such as a cell line for which a modification writing enzyme was knocked-down or knocked-out. Alternatively, on a smaller scale transcripts of interests could be synthesized in-vitro 2 5 7 27 839 0 0 0 0 5 5 365 371 0 0 0 0 1210 392 12 10 +nanoplot nanoplot html, tabular Plotting tool for long read sequencing data and alignments 2018-09-24 https://github.com/wdecoster/NanoPlot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ nanoplot 1.47.1 To update Visualization Scatter plot plotting, Box-Whisker plot plotting Scatter plot plotting, Box-Whisker plot plotting Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanoplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nanoplot nanoplot NanoPlot NanoPlot is a tool with various visualizations of sequencing data in bam, cram, fastq, fasta or platform-specific TSV summaries, mainly intended for long-read sequencing from Oxford Nanopore Technologies and Pacific Biosciences microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/plasmid-metagenomics-nanopore 1 7663 7942 168514 173861 4903 5029 72856 74900 2940 2983 25741 26566 295 297 3814 3828 279155 270925 16251 15801 +nanopolishcomp nanopolishcomp_eventaligncollapse, nanopolishcomp_freqmethcalculate tabular, txt, bed NanopolishComp contains 2 modules. Eventalign_collapse collapses the raw file generated by nanopolish eventalign by kmers rather than by event. Freq_meth_calculate methylation frequency at genomic CpG sites from the output of nanopolish call-methylation. 2020-04-27 https://a-slide.github.io/NanopolishComp 0.6.11 nanopolishcomp 0.6.12 To update Sequence Analysis Methylation analysis, Collapsing methods Methylation analysis, Collapsing methods Sequence analysis, Sequencing, Genetic variation Sequence analysis, Sequencing, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nanopolishcomp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nanopolishcomp nanopolishcomp NanopolishComp NanopolishComp is a Python3 package for downstream analyses of Nanopolish output files.It is a companion package for Nanopolish. 2 36 38 709 1129 0 0 0 0 0 0 0 0 1 1 1 1 1130 710 39 37 +ncbi_acc_download ncbi_acc_download txt Download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API 2019-11-06 https://github.com/kblin/ncbi-acc-download 0.2.8 ncbi-acc-download 0.2.8 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_acc_download /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ncbi_acc_download https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://usegalaxy.eu/published/workflow?id=a018307be3563f28 1 2027 2167 9533 10236 4656 5221 17731 19952 1153 1204 6985 7379 47 49 329 345 37912 34578 8641 7883 +ncbi_datasets datasets_download_gene, datasets_download_genome tabular, fasta NCBI datasets downloads biological sequence data across all domains of life from NCBI. 2022-01-27 https://github.com/ncbi/datasets 18.30.1 ncbi-datasets-cli To update Data Source Data handling, Sequence database search, Data retrieval Data handling, Sequence database search, Data retrieval Biological databases Biological databases iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_datasets /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ncbi_datasets ncbi_datasets NCBI Datasets NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases. Find and download sequence, annotation, and metadata for genes and genomes using our command-line tools or web interface. https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 2 1310 1310 6574 6574 3022 3022 17889 17889 2 2 3 3 88 88 425 425 24891 24891 4422 4422 +ncbi_entrez_direct ncbi_entrez_direct_efetch, ncbi_entrez_direct_einfo, ncbi_entrez_direct_esearch txt, xml NCBI Entrez Direct allow fetching data from NCBI Databases 2022-03-22 http://www.ncbi.nlm.nih.gov/books/NBK179288/ 22.4 entrez-direct 25.3 To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_direct /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ncbi_entrez_direct 3 0 0 0 0 0 1 0 3 0 0 0 0 0 0 0 0 3 0 1 0 +ncbi_entrez_eutils ncbi_eutils_ecitmatch, ncbi_eutils_efetch, ncbi_eutils_einfo, ncbi_eutils_elink, ncbi_eutils_epost, ncbi_eutils_esearch, ncbi_eutils_esummary tabular, xml, json NCBI Entrez E-Utilties allow fetching data from NCBI Databases 2015-04-14 https://www.ncbi.nlm.nih.gov/books/NBK25501/ 1.70 biopython 1.70 Up-to-date Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_entrez_eutils /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ncbi_entrez_eutils 7 242 422 2452 3350 0 0 0 0 0 0 0 0 0 0 0 0 3350 2452 422 242 +ncbi_fcs_gx ncbi_fcs_gx tabular, fasta FCS-GX detects contamination from foreign organisms in genome sequences using the genome cross-species aligner (GX). 2023-09-21 https://github.com/ncbi/fcs-gx 0.5.5 ncbi-fcs-gx 0.5.5 Up-to-date Sequence Analysis Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence assembly validation, Sequence trimming, Sequence contamination filtering Sequence analysis, Sequence assembly Sequence analysis, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ncbi_fcs_gx /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ncbi_fcs_gx ncbi_fcs NCBI fcs The NCBI Foreign Contamination Screen (FCS) is a tool suite for identifying and removing contaminant sequences in genome assemblies. Contaminants are defined as sequences in a dataset that do not originate from the biological source organism and can arise from a variety of environmental and laboratory sources. FCS will help you remove contaminants from genomes before submission to GenBank. 1 175 175 2259 2259 485 485 26859 26859 27 27 955 955 1 1 9 9 30082 30082 688 688 +necat necat fasta.gz, fasta Error correction and de-novo assembly for ONT Nanopore reads 2021-11-29 https://github.com/xiaochuanle/NECAT 0.0.1_update20200803 necat 0.0.1_update20200803 Up-to-date Assembly De-novo assembly De-novo assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/necat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/necat necat NECAT NECAT is an error correction and de-novo assembly tool for Nanopore long noisy reads. 1 228 228 1106 1106 0 0 0 0 0 0 0 0 0 0 0 0 1106 1106 228 228 +neighbors neighbors tabular Identify target and neighbor genomes for marker discovery 2026-03-31 https://github.com/EvolBioInf/neighbors 0.1.0 To update Phylogenetics, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/neighbors /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/neighbors 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +newick_utils newick_display svg Perform operations on Newick trees 2018-10-01 https://github.com/tjunier/newick_utils 1.6 newick_utils 1.6 Up-to-date Visualization, Metagenomics Phylogenetic tree generation, Phylogenetic tree analysis, Phylogenetic tree reconstruction Phylogeny, Genomics, Computer science Phylogeny, Genomics, Computer science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/newick_utils /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/newick_utils newick_utilities Newick Utilities The Newick Utilities are a set of command-line tools for processing phylogenetic trees. They can process arbitrarily large amounts of data and do not require user interaction, which makes them suitable for automating phylogeny processing tasks. microbiome/mothur-miseq-sop, microbiome/mothur-miseq-sop-short, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1756 1893 51682 53373 2196 2332 18983 20195 1114 1145 9635 9912 48 49 310 312 83792 80610 5419 5114 +nextclade nextalign, nextclade fasta, csv, tabular, json Identify differences between your sequences and a reference sequence used by Nextstrain 2021-03-29 https://github.com/nextstrain/nextclade 2.7.0 nextalign 2.14.0 To update Sequence Analysis Methylation analysis, Variant calling Methylation analysis, Variant calling Genomics, Sequence analysis, Cladistics Genomics, Cladistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nextclade /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nextclade nextclade Nextclade Nextclade is an open-source project for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. 2 373 373 4718 4718 309 309 11632 11632 258 258 2460 2460 11 11 723 723 19533 19533 951 951 +ngmlr ngmlr sam CoNvex Gap-cost alignMents for Long Reads 2020-10-27 https://github.com/philres/ngmlr @VERSION@ ngmlr 0.2.7 To update Next Gen Mappers DNA mapping, Sequence alignment, Genetic variation analysis DNA mapping, Sequence alignment, Genetic variation analysis Sequencing, Mapping, DNA structural variation Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngmlr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ngmlr ngmlr NGMLR An algorithm to map third generation long-read sequencing data (PacBio and Oxford Nanopore) to a reference genome with a focus on reads that span structural variation. 1 53 53 1408 1408 0 0 0 0 0 0 0 0 0 0 0 0 1408 1408 53 53 +ngsderive ngsderive_strandedness tabular Forensic analysis tool for inferring properties from NGS data 2026-01-07 https://github.com/stjudecloud/ngsderive @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ngsderive 4.0.0 To update Sequence Analysis, RNA, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsderive /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ngsderive 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ngsutils ngsutils_bam_filter bam NGSUtils is a suite of software tools for working with next-generation sequencing datasets.Starting in 2009, we (Liu Lab @ Indiana University School of Medicine) starting working withnext-generation sequencing data. We initially started doing custom coding for each project in a one-off manner.It quickly became apparent that this was an inefficient manner to work, so we started assembling smallerutilities that could be adapted into larger, more complicated, workflows. We have used them for Illumia,SOLiD, 454, Ion Torrent, and Pac Bio sequencing data. We have used them for DNA and RNA resequcing,ChIP-Seq, CLIP-Seq, and targeted resequencing (Agilent exome capture and PCR targeting).These tools are also used heavily in our in-house DNA and RNA mapping pipelines.NGSUtils is made up of 50+ programs, mainly written in Python.These are separated into modules based on the type of file that is to be analyzed. 2015-11-10 https://github.com/ngsutils/ngsutils @WRAPPER_VERSION@ ngsutils 0.5.9 To update SAM Read pre-processing, Sequencing quality control, Variant calling, Formatting, Sequence contamination filtering Read pre-processing, Variant calling, Formatting, Sequence contamination filtering Genomics, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ngsutils /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ngsutils ngsutils NGSUtils NGSUtils is a suite of software tools for working with next-generation sequencing datasets microbiome/metagenomics-assembly 1 702 894 27862 37369 902 1390 17094 25161 128 176 10945 13368 21 21 148 148 76046 56049 2481 1753 +nlp_cooccurrence_analysis nlp_cooccurrence_analysis tabular Co-occurrence analysis from NLP-annotated JSON 2026-05-19 https://github.com/galaxyproject/tools-iuc/tree/main/tools/cooccurrence @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Text Manipulation, Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/cooccurrence /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/cooccurrence 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +nonpareil nonpareil tabular, txt, json Estimate average coverage in metagenomic datasets 2017-11-03 http://nonpareil.readthedocs.io 3.5.5 nonpareil 3.5.5 Up-to-date Metagenomics Operation Operation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nonpareil /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nonpareil nonpareil nonpareil Estimate metagenomic coverage and sequence diversity 1 16 19 105 195 23 26 122 168 0 0 0 0 0 0 0 0 363 227 45 39 +novoplasty novoplasty fasta, txt, vcf, tabular NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. 2020-05-18 https://github.com/ndierckx/NOVOPlasty @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ novoplasty 4.3.5 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/novoplasty /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/novoplasty 1 502 502 11073 11073 1 1 1 1 137 137 3542 3542 11 11 37 37 14653 14653 651 651 +nugen_nudup nugen_nudup bam, txt Marks/removes PCR introduced duplicate molecules based on the molecular tagging technology used in NuGEN products. 2016-11-18 https://github.com/tecangenomics/nudup 2.3.3 nudup 2.3.3 Up-to-date SAM, Metagenomics, Sequence Analysis, Transcriptomics Duplication detection, Sequence analysis Duplication detection, Sequence analysis Sequencing, Genomics Sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/nugen_nudup /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/nugen_nudup nudup NuDup Marks/removes duplicate molecules based on the molecular tagging technology used in Tecan products. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +obitools obi_annotate, obi_clean, obi_complement, obi_convert, obi_grep, obi_multiplex, obi_pairing, obi_pcr, obi_refidx, obi_tag, obi_taxonomy, obi_uniq csv, fasta OBITools is a set of programs developed to simplify the manipulation of sequence files 2017-03-22 https://github.com/metabarcoding/obitools4 4.4.45 obitools4 4.4.45 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/obitools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/obitools 12 329 331 30430 30600 0 0 0 0 49 49 2343 2343 11 11 202 202 33145 32975 391 389 +ococo ococo vcf, fasta, pileup Variant detection of SNVs 2017-12-07 https://github.com/karel-brinda/ococo 0.1.2.6 ococo 0.1.2.7 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ococo /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ococo 1 71 101 1253 2070 186 208 1426 1552 0 0 0 0 0 0 0 0 3622 2679 309 257 +odgi odgi_build, odgi_viz odgi, gfa1, png Representing large genomic variation graphs with minimal memory overhead requires a careful encoding of the graph entities. odgi follows the dynamic GBWT in developing a byte-packed version of the graph and paths through it. 2020-04-07 https://github.com/vgteam/odgi 0.3 odgi 0.9.4 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/odgi /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/odgi 2 3 4 7 29 0 0 0 0 0 0 0 0 0 0 0 0 29 7 4 3 +omark omark txt, omq, pdf, png, sum, ump Proteome quality assessment software 2023-11-15 https://github.com/DessimozLab/OMArk 0.3.1 To update Sequence Analysis Sequence assembly validation, Differential protein expression profiling Sequence assembly validation, Differential protein expression profiling Proteomics, Sequence analysis, Statistics and probability Proteomics, Sequence analysis, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/omark /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/omark omark OMArk OMArk is a software for proteome (protein-coding gene repertoire) quality assessment. It provides measures of proteome completeness, characterizes the consistency of all protein coding genes with regard to their homologs, and identifies the presence of contamination from other species. OMArk relies on the OMA orthology database, from which it exploits orthology relationships, and on the OMAmer software for fast placement of all proteins into gene families. 1 89 89 707 707 17 17 44 44 6 6 11 11 15 15 347 347 1109 1109 127 127 +ont_fast5_api ont_fast5_api_compress_fast5, ont_fast5_api_fast5_subset, ont_fast5_api_multi_to_single_fast5, ont_fast5_api_single_to_multi_fast5 ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore FAST5 file format. 2020-06-08 https://github.com/nanoporetech/ont_fast5_api/ 3.1.3 ont-fast5-api 4.1.3 To update Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ont_fast5_api /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ont_fast5_api 4 49 51 2529 3106 0 0 0 0 0 0 0 0 0 0 0 0 3106 2529 51 49 +onto_toolkit onto_tk_get_ancestor_terms, onto_tk_get_child_terms, onto_tk_get_descendent_terms, onto_tk_get_parent_terms, onto_tk_get_parent_terms_by_relationship_type, onto_tk_get_relationship_id_vs_relationship_def, onto_tk_get_relationship_id_vs_relationship_name, onto_tk_get_relationship_id_vs_relationship_namespace, onto_tk_get_relationship_types, onto_tk_get_root_terms, onto_tk_get_subontology_from, onto_tk_term_id_vs_term_def, onto_tk_term_id_vs_term_name, onto_tk_get_term_synonyms, onto_tk_get_terms, onto_tk_get_terms_by_relationship_type, onto_tk_obo2owl, onto_tk_obo2rdf, onto_tk_term_id_vs_term_def tabular, obo, owl, rdf ONTO-Toolkit is a collection of tools for managing ontologies. 2017-11-04 http://search.cpan.org/~easr/ONTO-PERL-1.45/ 1.45 perl-onto-perl 1.45 Up-to-date Ontology Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/onto_toolkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/onto_toolkit 17 8 11 75 666 0 0 0 0 0 0 0 0 0 0 0 0 666 75 11 8 +openalex_explorer openalex_explorer tabular Fetch citing papers from OpenAlex using DOI, ID and title 2025-05-29 https://openalex.org/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/openalex /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/openalex 1 3 3 8 8 0 0 0 0 0 0 0 0 0 0 0 0 8 8 3 3 +optdoe optdoe xml Optimal Design Of Experiment 2022-10-27 https://github.com/pablocarb/doebase @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ doebase To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/optdoe /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/optdoe 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +optitype optitype pdf, tabular Precision HLA typing from NGS data 2021-02-17 https://github.com/FRED-2/OptiType @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ optitype 1.5.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/optitype /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/optitype 1 62 62 585 585 18 18 99 99 6 6 97 97 0 0 0 0 781 781 86 86 +orfipy orfipy bed6, bed12, fasta Galaxy wrapper for ORFIPY 2022-04-07 https://github.com/urmi-21/orfipy 0.0.4 orfipy 0.0.4 Up-to-date Sequence Analysis Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Coding region prediction, Database search, Transcriptome assembly, De-novo assembly Computer science, RNA-Seq, Transcriptomics, Small molecules Computer science, RNA-Seq, Transcriptomics, Small molecules iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orfipy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/orfipy orfipy orfipy A fast and flexible tool for extracting ORFs.orfipy is a tool written in python/cython to extract ORFs in extremely an fast and flexible manner. Other popular ORF searching tools are OrfM and getorf. Compared to OrfM and getorf, orfipy provides the most options to fine tune ORF searches. orfipy uses multiple CPU cores and is particularly faster for data containing multiple smaller fasta sequences such as de-novo transcriptome assemblies. Please read the preprint here. 1 172 172 1509 1509 343 343 2776 2776 0 0 0 0 0 0 0 0 4285 4285 515 515 +orthofinder orthofinder_onlygroups txt, tsv, newick Accurate inference of orthologous gene groups made easy 2017-05-22 https://github.com/davidemms/OrthoFinder 2.5.5 orthofinder 3.1.5 To update Phylogenetics, Sequence Analysis Genome comparison, Phylogenetic tree generation (from molecular sequences), Phylogenetic tree analysis, Genome alignment Genome comparison, Genome alignment Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics, Sequence analysis Phylogenetics, Phylogenomics, Bioinformatics, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/orthofinder /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/orthofinder OrthoFinder OrthoFinder OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthogroups and orthologs, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees. It also infers a rooted species tree for the species being analysed and maps the gene duplication events from the gene trees to branches in the species tree. OrthoFinder also provides comprehensive statistics for comparative genomic analyses. 1 801 801 3870 3870 0 0 0 0 133 133 1450 1450 36 36 221 221 5541 5541 970 970 +packaged_annotation_loader packaged_annotation_loader tabular Tool to make cached genome annotation data available as a list of datasets collection 2022-01-04 https://github.com/galaxyproject/tools-iuc/tree/master/tools/packaged_annotation_loader 0.1 python To update Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/packaged_annotation_loader /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/packaged_annotation_loader 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pacu pacu_map, pacu_snp bam, html PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data. 2024-08-13 https://github.com/BioinformaticsPlatformWIV-ISP/PACU 0.0.5 pacu_snp 1.0.0 To update Sequence Analysis, Phylogenetics Clustering Clustering Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pacu /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pacu pacu PACU PACU is a workflow for whole genome sequencing based phylogeny of Illumina and ONT R9/R10 data.PACU stands for the Prokaryotic Awesome variant Calling Utility and is named after an omnivorous fish (that eats both Illumina and ONT reads). 2 19 19 223 223 0 0 0 0 0 0 0 0 0 0 0 0 223 223 19 19 +page_dewarp page_dewarp png Page dewarping and thresholding of document images using a cubic sheet model 2026-05-07 https://github.com/lmmx/page-dewarp 0.3.4 page-dewarp To update Imaging, Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/page_dewarp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/page_dewarp 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pairtools pairtools_dedup, pairtools_parse, pairtools_sort, pairtools_split, pairtools_stats tabular, 4dn_pairsam, qname_sorted.bam Flexible tools for Hi-C data processing 2024-03-26 https://pairtools.readthedocs.io 1.1.3 pairtools 1.1.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pairtools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pairtools https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 5 25 25 742 742 8 8 415 415 0 0 0 0 0 0 0 0 1157 1157 33 33 +pal2nal pal2nal txt, html Wraps PAL2NAL to convert protein alignments and nucleotide FASTA into codon-aware alignments. 2025-11-09 http://www.bork.embl.de/pal2nal @TOOL_VERSION@+galaxy@WRAPPER_VERSION@ pal2nal 14.1 To update Sequence Analysis, Phylogenetics iuc https://github.com/georgehe23/tools-iuc/tree/main/tools/pal2nal /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pal2nal 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +panaroo panaroo txt A Bacterial Pangenome Analysis Pipeline 2025-02-28 https://github.com/gtonkinhill/panaroo/releases 1.7.0 panaroo 1.7.0 Up-to-date Sequence Analysis De-novo assembly, Genome assembly, Clustering De-novo assembly, Genome assembly, Clustering Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing Workflows, Sequence assembly, Gene and protein families, Plant biology, Sequencing galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/panaroo /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/panaroo panaroo Panaroo Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. 1 67 67 297 297 0 0 0 0 39 39 312 312 0 0 0 0 609 609 106 106 +pangolin pangolin tabular, fasta Pangolin assigns SARS-CoV-2 genome sequences their most likely lineages under the Pango nomenclature system. 2021-03-06 https://github.com/cov-lineages/pangolin @TOOL_VERSION@ pangolin 4.4 To update Sequence Analysis Tree-based sequence alignment, Variant classification Tree-based sequence alignment, Variant classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pangolin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pangolin pangolin_cov-lineages pangolin Phylogenetic Assignment of Named Global Outbreak LINeages - software package for assigning SARS-CoV-2 genome sequences to global lineages 1 595 595 7737 7737 416 416 9068 9068 277 277 3099 3099 12 12 603 603 20507 20507 1300 1300 +panta panta json, tsv, csv, txt, fasta Efficient inference of large prokaryotic pangenomes with PanTA. 2025-09-15 https://github.com/amromics/panta 1.0.1 panta 1.0.1 Up-to-date Genome annotation, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/panta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/panta 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +parse_mito_blast parse_mito_blast tabular, txt Filtering blast out from querying assembly against mitochondrial database. 2022-05-12 https://raw.githubusercontent.com/VGP/vgp-assembly/master/galaxy_tools/parse_mito_blast/parse_mito_blast.py @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ parse_mito_blast 1.0.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/parse_mito_blast /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/parse_mito_blast 1 136 136 1872 1872 95 95 1193 1193 33 33 178 178 0 0 0 0 3243 3243 264 264 +pathview pathview png, pdf Pathview is a tool set for pathway based data integration and visualization. 2019-08-26 https://bioconductor.org/packages/release/bioc/html/pathview.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-pathview 1.50.0 To update Statistics, RNA, Micro-array Analysis Pathway or network analysis, Pathway or network visualisation Pathway or network analysis, Pathway or network visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation Molecular interactions, pathways and networks, Systems biology, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pathview /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pathview pathview pathview Tool set for pathway based data integration and visualization that maps and renders a wide variety of biological data on relevant pathway graphs. It downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, it integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis. 1 1546 1688 8322 9128 1410 1484 7998 8673 244 244 1526 1526 21 22 258 275 19602 18104 3438 3221 +pbgcpp pbgcpp fasta, gff, vcf Compute genomic consensus and call variants using PacBio reads mapped to a reference 2022-03-11 https://github.com/PacificBiosciences/gcpp 2.0.2 pbgcpp 2.0.2 Up-to-date Variant Analysis Variant calling Variant calling Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbgcpp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pbgcpp genomicconsensus GenomicConsensus The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pbmm2 pbmm2 bam A minimap2 SMRT wrapper for PacBio data. 2022-03-11 https://github.com/PacificBiosciences/pbmm2 26.1.99 pbmm2 26.1.99 Up-to-date Next Gen Mappers Pairwise sequence alignment, Sorting Pairwise sequence alignment, Sorting Mapping Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pbmm2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pbmm2 pbmm2 pbmm2 pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments. Sorted output can be used directly for polishing using GenomicConsensus, if BAM has been used as input to pbmm2. Benchmarks show that pbmm2 outperforms BLASR in sequence identity, number of mapped bases, and especially runtime. pbmm2 is the official replacement for BLASR. 1 41 41 229 229 0 0 0 0 0 0 0 0 0 0 0 0 229 229 41 41 +pcdl pcdl_get_anndata, pcdl_get_cell_attribute, pcdl_get_cell_attribute_list, pcdl_get_cell_df, pcdl_get_celltype_list, pcdl_get_conc_attribute, pcdl_get_conc_df, pcdl_get_substrate_list, pcdl_get_unit_dict, pcdl_get_version, pcdl_make_cell_vtk, pcdl_make_conc_vtk, pcdl_make_gif, pcdl_make_graph_gml, pcdl_make_movie, pcdl_plot_contour, pcdl_plot_scatter, pcdl_plot_timeseries txt pcdl PhysiCell Data Loader. 2025-06-05 https://github.com/elmbeech/physicelldataloader 3.0.1 To update Systems Biology, Data Export, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pcdl /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pcdl 18 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pdfimages pdfimages PDF image extractor. 2025-07-31 https://gitlab.freedesktop.org/poppler/poppler/ 25.07.0 poppler To update Imaging, Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pdfimages /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pdfimages 1 2 2 15 15 0 0 0 0 0 0 0 0 0 0 0 0 15 15 2 2 +pe_histogram pe_histogram png, tabular Contains a tool that produces an insert size histogram for a paired-end BAM file. 2016-06-16 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/pehistogram 1.0.2 openjdk To update Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pe_histogram /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pe_histogram https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379 1 709 709 8778 8778 1037 1176 10416 11753 168 168 1076 1076 72 72 195 195 21802 20465 2125 1986 +peakzilla peakzilla tabular, txt Peakzilla identifies sites of enrichment and transcription factor binding sites from ChIP-seq and ChIP-exo experiments. 2024-02-25 https://github.com/steinmann/peakzilla @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/peakzilla /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/peakzilla 1 19 19 73 73 0 0 0 0 0 0 0 0 0 0 0 0 73 73 19 19 +pear iuc_pear auto PEAR evaluates all possible paired-end read overlaps 2015-02-11 https://cme.h-its.org/exelixis/web/software/pear/ @TOOL_VERSION@.@VERSION_SUFFIX@ pear 0.9.11 To update Fastq Manipulation Sequence merging Sequence merging Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pear /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pear pear PEAR Paired-end read merger. PEAR evaluates all possible paired-end read overlaps without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. 1 416 448 9796 10458 665 1869 8692 23290 202 335 4780 8865 0 0 0 0 42613 23268 2652 1283 +pgxrpi pgx_freqplot, pgx_loader pdf, txt pgxLoader and pgxFreqplot functions from pgxRpi 2025-02-27 https://github.com/progenetix/pgxRpi 1.2.0 bioconductor-pgxrpi 1.6.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pgxRpi /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pgxRpi 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pharokka pharokka genbank, gff, zip rapid standardised annotation tool for bacteriophage genomes and metagenomes 2023-02-14 https://github.com/gbouras13/pharokka 1.3.2 " + pharokka + " To update Genome annotation Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Genome annotation, Antimicrobial resistance prediction, tRNA gene prediction, Formatting, Sequence assembly Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA Metagenomics, Sequence sites, features and motifs, Workflows, Functional, regulatory and non-coding RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pharokka /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pharokka pharokka Pharokka Pharokka is a rapid standardised annotation tool for bacteriophage genomes and metagenomes. 1 766 766 16933 16933 1 1 21 21 117 117 1202 1202 0 0 0 0 18156 18156 884 884 +phyloseq phyloseq_add_rank_names, phyloseq_from_biom, phyloseq_from_dada2, phyloseq_plot_bar, phyloseq_plot_ordination, phyloseq_plot_richness, phyloseq_tax_glom phyloseq, pdf, tabular Handling and analysis of high-throughput microbiome census data 2022-03-03 https://www.bioconductor.org/packages/release/bioc/html/phyloseq.html 1.54.0 bioconductor-phyloseq 1.54.0 Up-to-date Metagenomics Deposition, Analysis, Visualisation Deposition, Analysis, Visualisation Microbiology, Sequence analysis, Metagenomics Microbiology, Sequence analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyloseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/phyloseq phyloseq phyloseq Provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data. microbiome/dada-16S 7 251 251 3161 3161 156 156 1022 1022 35 35 190 190 14 14 163 163 4536 4536 456 456 +phyml phyml nhx, txt PhyML is a phylogeny software based on the maximum-likelihood principle. 2019-05-27 http://www.atgc-montpellier.fr/phyml/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ phyml 3.3.20220408 To update Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods) Phylogenetics, Bioinformatics, Phylogenetics Phylogenetics, Bioinformatics, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/phyml /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/phyml phyml PhyML Phylogenetic estimation software using Maximum Likelihood 1 286 335 2452 2654 0 0 0 0 215 240 1475 1564 79 79 334 334 4552 4261 654 580 +picard picard_AddCommentsToBam, picard_AddOrReplaceReadGroups, picard_BedToIntervalList, picard_CleanSam, picard_CASM, picard_CollectBaseDistributionByCycle, picard_CollectGcBiasMetrics, picard_CollectHsMetrics, picard_CollectInsertSizeMetrics, picard_CollectRnaSeqMetrics, picard_artifact_metrics, picard_CollectWgsMetrics, picard_DownsampleSam, picard_EstimateLibraryComplexity, picard_FastqToSam, picard_FilterSamReads, picard_FixMateInformation, picard_MarkDuplicates, picard_MarkDuplicatesWithMateCigar, picard_MeanQualityByCycle, picard_MergeBamAlignment, picard_MergeSamFiles, picard_NormalizeFasta, picard_QualityScoreDistribution, picard_ReorderSam, picard_ReplaceSamHeader, picard_RevertOriginalBaseQualitiesAndAddMateCigar, picard_RevertSam, picard_SamToFastq, picard_SortSam, picard_ValidateSamFile bam, picard_interval_list, tabular, pdf, txt, unsorted.bam, fasta, fastqsanger Picard SAM/BAM manipulation tools. 2017-01-11 http://broadinstitute.github.io/picard/ 3.1.1 picard 3.4.0 To update SAM Formatting Formatting Sequencing Sequencing devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/picard /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/picard picard_samtofastq picard_samtofastq Create a FASTQ file. https://usegalaxy.eu/published/workflow?id=4daa0c33d6d50379 31 5984 6700 343073 472216 11191 18752 341066 667776 1462 1651 57833 72802 1018 1021 41496 41992 1254786 783468 28124 19655 +pick_value pick_value Compose a text parameter value using text, integer and float values 2023-01-23 0.2.0 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pick_value /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pick_value https://usegalaxy.eu/published/workflow?id=8be366ad6a42408b, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=95f420d8856bf725, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2, https://workflowhub.eu/workflows/612?version=12, https://workflowhub.eu/workflows/642?version=10 1 157 157 6779 6779 188 188 12737 12737 16 16 746 746 4 4 332 332 20594 20594 365 365 +picrust picrust_categorize, picrust_compare_biom, picrust_format_tree_and_trait_table, picrust_metagenome_contributions, picrust_normalize_by_copy_number, picrust_predict_metagenomes tabular, nhx PICRUSt wrappers 2016-11-08 https://picrust.github.io/picrust/ 1.1.1 picrust 1.1.4 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Phylogenetic reconstruction, Expression analysis, Genome annotation, DNA barcoding Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing Metagenomics, Microbial ecology, Functional, regulatory and non-coding RNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/picrust picrust PICRUSt PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. 6 44 63 562 1142 0 0 0 0 38 41 2348 2626 20 20 442 442 4210 3352 124 102 +picrust2 picrust2_add_descriptions, picrust2_hsp, picrust2_metagenome_pipeline, picrust2_pathway_pipeline, picrust2_pipeline, picrust2_place_seqs, picrust2_shuffle_predictions tabular PICRUSt2: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States 2021-07-09 https://github.com/picrust/picrust2/wiki 2.5.3 picrust2 2.6.3 To update Metagenomics Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Phylogenetic reconstruction, Expression analysis, Rarefaction, Pathway analysis Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing Metagenomics, Microbiology, Phylogenetics, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/picrust2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/picrust2 picrust2 PICRUSt2 PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences. 7 327 327 6432 6432 1 1 1 1 64 64 2888 2888 0 0 0 0 9321 9321 392 392 +pilon pilon vcf, txt, fasta pilon is a tool for assembly improvement and variant analysis in bacteria 2016-08-11 https://github.com/broadinstitute/pilon/wiki 1.20.1 pilon 1.24 To update Variant Analysis Sequence assembly, Analysis, Read alignment Sequence assembly, Analysis Assembly Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pilon /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pilon pilon pilon Read alignment analysis to diagnose, report, and automatically improve de novo genome assemblies. 1 1417 1484 10881 12166 1340 1411 8461 9526 985 1018 5002 5466 25 25 126 126 27284 24470 3938 3767 +pimento pimento_are_there_primers, pimento_auto, pimento_choose_primer_cutoff, pimento_find_cutoffs, pimento_gen_bcv, pimento_std txt, fasta, tsv A PrIMEr infereNce TOolkit to facilitate large-scale calling of metabarcoding amplicon sequence variants. 2025-08-04 https://github.com/EBI-Metagenomics/PIMENTO 1.0.3 mi-pimento 1.0.3 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pimento /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pimento 6 1 1 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 1 1 +pipelign pipelign fasta Multipe sequence alignment 2019-08-20 https://github.com/asmmhossain/pipelign/ @VERSION@ pipelign 0.2 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pipelign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pipelign 1 313 329 1909 1972 715 796 9356 9994 0 0 0 0 0 0 0 0 11966 11265 1125 1028 +pirate pirate txt, tsv, fasta, newick, gfa1, gff, pdf Pangenome Iterative Refinement and Threshold Evaluation. 2026-01-31 https://github.com/SionBayliss/PIRATE 1.0.5 pirate 1.0.5 Up-to-date Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pirate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pirate 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +pizzly pizzly tabular, fasta Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. 2017-09-03 https://github.com/pmelsted/pizzly/ 0.37.3.1 pizzly 0.37.3 To update Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pizzly /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pizzly 1 25 30 2337 2381 71 89 2125 2362 0 0 0 0 0 0 0 0 4743 4462 119 96 +plasclass plasclass tabular PlasClass is a tool to classify sequences of plasmid or chromosomal origin 2025-07-31 https://github.com/Shamir-Lab/PlasClass @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasclass 0.1.1 To update Sequence Analysis Sequence classification, Sequence assembly, k-mer counting Sequence classification, Sequence assembly, k-mer counting Metagenomics, Sequence assembly, DNA, Metagenomic sequencing Metagenomics, Sequence assembly, DNA, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasclass /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/plasclass PlasClass PlasClass PlasClass is a tool for easy classification of sequences as either plasmid or chromosomal. For example, it can be used to classify the contigs in a (metagenomic) assembly. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +plasflow PlasFlow tabular, fasta PlasFlow - Prediction of plasmid sequences in metagenomic contigs. 2018-09-05 https://github.com/smaegol/PlasFlow @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plasflow 1.1.0 To update Sequence Analysis Sequence analysis Sequence analysis Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning Metagenomics, Sequence assembly, Mobile genetic elements, Machine learning iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasflow /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/plasflow plasflow PlasFlow PlasFlow is a set of scripts used for prediction of plasmid sequences in metagenomic contigs. microbiome/plasmid-metagenomics-nanopore 1 876 1004 55069 56639 757 797 7929 8195 87 87 3496 3496 0 0 0 0 68330 66494 1888 1720 +plasmidfinder plasmidfinder json, fasta, tabular, txt Identify plasmids in total or partial sequenced isolates of bacteria. 2022-09-19 https://bitbucket.org/genomicepidemiology/plasmidfinder/src/master/ 2.1.6 plasmidfinder 2.1.6 Up-to-date Sequence Analysis Genome assembly, Scaffolding, Multilocus sequence typing Genome assembly, Scaffolding, Multilocus sequence typing Whole genome sequencing, Sequence assembly, Mapping, Probes and primers Whole genome sequencing, Sequence assembly, Mapping, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plasmidfinder /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/plasmidfinder PlasmidFinder PlasmidFinder PlasmidFinder is a tool for the identification and typing of Plasmid Replicons in Whole-Genome Sequencing (WGS). 1 1015 1015 35994 35994 623 623 11939 11939 211 211 3278 3278 48 48 10730 10730 61941 61941 1897 1897 +plink plink pbed, txt, tabular Whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 2020-09-14 https://www.cog-genomics.org/plink @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ plink 1.90b6.21 To update Genome-Wide Association Study Genetic variation analysis Genetic variation analysis GWAS study GWAS study iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/plink /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/plink plink PLINK Free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 1 191 191 1210 1210 105 105 1251 1251 0 0 0 0 7 7 67 67 2528 2528 303 303 +polypolish polypolish fasta, tabular, txt """Polypolish is a tool for polishing genome assemblies with short reads.Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location).This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix.""" 2022-09-22 https://github.com/rrwick/Polypolish 0.6.1 polypolish 0.6.1 Up-to-date Sequence Analysis Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Genome assembly, Read mapping, Mapping assembly, Sequencing error detection Sequence assembly, Sequence composition, complexity and repeats, Mapping Sequence assembly, Sequence composition, complexity and repeats, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/polypolish /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/polypolish Polypolish Polypolish Polypolish is a tool for polishing genome assemblies with short reads. Unlike other tools in this category, Polypolish uses SAM files where each read has been aligned to all possible locations (not just a single best location). This allows it to repair errors in repeat regions that other alignment-based polishers cannot fix. 1 147 147 1066 1066 0 0 0 0 26 26 615 615 10 10 79 79 1760 1760 183 183 +porechop porechop fasta, txt Porechop - Finding and removing adapters from Oxford Nanopore reads 2018-09-13 https://github.com/rrwick/Porechop @WRAPPER_VERSION@ porechop 0.2.4 To update Fasta Manipulation, Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/porechop /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/porechop microbiome/beer-data-analysis, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data 1 3888 4063 445549 452222 3090 3144 150171 150874 1362 1432 46371 65797 9 9 10935 10935 679828 653026 8648 8349 +poretools poretools_events, poretools_extract, poretools_hist, poretools_nucdist, poretools_occupancy, poretools_qualdist, poretools_qualpos, poretools_squiggle, poretools_stats, poretools_tabular, poretools_times, poretools_winner, poretools_yield_plot tabular, fastq, txt A flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 2017-12-17 https://poretools.readthedocs.io/en/latest/ 0.6.1a1 poretools 0.6.1a1 Up-to-date Fasta Manipulation, Fastq Manipulation Nucleic acid sequence analysis Nucleic acid sequence analysis DNA, Sequencing DNA, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/poretools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/poretools poretools Poretools Flexible toolkit for exploring datasets generated by nanopore sequencing devices from MinION for the purposes of quality control and downstream analysis. 13 172 274 15702 21152 392 508 31358 42781 125 130 9684 11349 0 0 0 0 75282 56744 912 689 +ppanggolin ppanggolin_all, ppanggolin_msa, ppanggolin_projection, ppanggolin_rarefaction tsv, fasta, json, xml, html, csv, txt, h5, tar.gz, tabular Microbial Partitioned PanGenome 2025-01-22 https://github.com/labgem/PPanGGOLiN 2.3.0 ppanggolin 2.3.0 Up-to-date Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Rarefaction, Essential dynamics, Sequence assembly, Genome annotation Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping Metagenomics, Gene and protein families, Model organisms, Public health and epidemiology, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ppanggolin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ppanggolin ppanggolin PPanGGOLiN PPanGGOLiN is a software suite used to create and manipulate prokaryotic pangenomes from a set of either genomic DNA sequences or provided genome annotations. It is designed to scale up to tens of thousands of genomes. It has the specificity to partition the pangenome using a statistical approach rather than using fixed thresholds which gives it the ability to work with low-quality data such as Metagenomic Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) thus taking advantage of large scale environmental studies and letting users study the pangenome of uncultivable species 4 55 55 249 249 0 0 0 0 0 0 0 0 16 16 67 67 316 316 71 71 +preseq preseq_c_curve, preseq_lc_extrap tsv Wrapper for Preseq tool suite (c_curve, lc_extrap) 2026-03-11 https://github.com/smithlabcode/preseq 3.2.0 preseq 3.2.0 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/preseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/preseq 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +presto presto_alignsets, presto_assemblepairs, presto_buildconsensus, presto_collapseseq, presto_filterseq, presto_maskprimers, presto_pairseq, presto_parseheaders, presto_parselog, presto_partition, prestor_abseq3 fastq, tsv, html pRESTO toolkit for immune repertoire analysis. 2017-08-30 https://presto.readthedocs.io/ 0.6.2 presto 0.7.9 To update Sequence Analysis Nucleic acid sequence analysis Nucleic acid sequence analysis Sequencing, DNA, Immunology Sequencing, DNA, Immunology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/presto /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/presto presto pRESTO Integrated collection of platform-independent Python modules for processing raw reads from high-throughput (next-generation) sequencing of lymphocyte repertoires. 11 0 0 0 0 331 401 75739 81623 0 0 0 0 0 0 0 0 81623 75739 401 331 +prinseq prinseq PRINSEQ is a tool for easy and rapid quality control and data processing of metagenomic and metatranscriptomic datasets 2016-05-30 http://prinseq.sourceforge.net/manual.html @TOOL_VERSION prinseq 0.20.4 To update Fastq Manipulation, Metagenomics Read pre-processing, Sequence trimming, Sequence contamination filtering Read pre-processing, Sequence trimming, Sequence contamination filtering Transcriptomics, Metagenomics, Genomics Transcriptomics, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prinseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/prinseq prinseq PRINSEQ PRINSEQ is a sequence processing tool that can be used to filter, reformat and trim genomic and metagenomic sequence data. It generates summary statistics of the input in graphical and tabular formats that can be used for quality control steps. PRINSEQ is available as both standalone and web-based versions. https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c 1 345 412 15643 16651 1317 1501 10523 12474 0 0 0 0 11 11 17 17 29142 26183 1924 1673 +prodigal prodigal genbank, fasta, tabular A protein-coding gene prediction software tool for bacterial and archaeal genomes 2024-03-14 https://github.com/hyattpd/Prodigal @VERSION@ prodigal 2.6.3 To update Genome annotation Genome annotation Genome annotation Genomics, Sequence analysis Genomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prodigal /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/prodigal prodigal Prodigal Fast, reliable protein-coding gene prediction for prokaryotic genomes. 1 611 611 6456 6456 0 0 0 0 70 70 1515 1515 19 19 1487 1487 9458 9458 700 700 +progressivemauve progressivemauve, xmfa2gff3 xmfa, nhx, tabular, gff3 Mauve/ProgressiveMauve Multiple Sequence Aligner 2015-05-15 http://darlinglab.org/mauve/user-guide/progressivemauve.html @WRAPPER_VERSION@.1 progressivemauve snapshot_2015_02_13 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/progressivemauve /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/progressivemauve 2 788 861 2637 3053 1096 1189 3329 3750 0 0 0 0 1 1 1 1 6804 5967 2051 1885 +prokka prokka gff3, genbank, fasta, asn1, txt, tabular Rapid annotation of prokaryotic genomes 2016-10-07 http://github.com/tseemann/prokka @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ prokka 1.15.6 To update Sequence Analysis Gene prediction, Coding region prediction, Genome annotation Coding region prediction, Genome annotation Genomics, Model organisms, Virology Genomics, Model organisms, Virology crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/prokka /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/prokka prokka Prokka Software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files. 1 10459 11098 819587 847581 14547 16587 462648 506432 5094 6142 199279 229418 422 424 7463 7481 1590912 1488977 34251 30522 +prot_scriber prot_scriber tabular Protein annotation of short human readable descriptions 2022-05-10 https://github.com/usadellab/prot-scriber @TOOL_VERSION@ prot-scriber 0.1.6 To update Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/prot-scriber /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/prot-scriber 1 9 9 13 13 0 0 0 0 0 0 0 0 0 0 0 0 13 13 9 9 +proteinortho proteinortho, proteinortho_clustering, proteinortho_grab_proteins, proteinortho_summary tabular Proteinortho is a tool to detect orthologous proteins/genes within different species. 2020-02-05 https://gitlab.com/paulklemm_PHD/proteinortho 6.3.6 proteinortho 6.3.6 Up-to-date Proteomics Sequence clustering, Sequence analysis Sequence clustering, Sequence analysis Comparative genomics Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/proteinortho /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/proteinortho proteinortho Proteinortho Proteinortho is a tool to detect orthologous genes within different species 4 432 463 5028 5485 0 0 0 0 0 0 0 0 4 4 23 23 5508 5051 467 436 +psauron psauron csv PSAURON is a machine learning model for rapid assessment of protein coding gene annotation 2026-02-20 https://github.com/salzberg-lab/PSAURON/ 1.1.3 psauron 1.1.3 Up-to-date Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/psauron /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/psauron 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +psiclass psiclass gtf, interval PsiCLASS is a reference-based transcriptome assembler for single or multiple RNA-seq samples. 2023-09-06 https://github.com/splicebox/PsiCLASS 1.0.3 psiclass 1.0.3 Up-to-date Transcriptomics Transcriptome assembly Transcriptome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/psiclass /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/psiclass psiclass PsiCLASS Reference-based transcriptome assembler for single or multiple RNA-seq samples 1 11 11 46 46 0 0 0 0 0 0 0 0 0 0 0 0 46 46 11 11 +pureclip pureclip bed, txt PureCLIP is an HMM based peak caller specifically designed for eCLIP/iCLIP data 2018-04-26 https://github.com/skrakau/PureCLIP @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ pureclip 1.3.1 To update Sequence Analysis, RNA, CLIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pureclip /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pureclip 1 84 105 1337 1705 0 0 0 0 0 0 0 0 0 0 0 0 1705 1337 105 84 +purge_dups purge_dups tabular, wig, png, txt, bed Purge haplotigs and overlaps in an assembly based on read depth 2021-02-03 https://github.com/dfguan/purge_dups 1.2.6 purge_dups 1.2.6 Up-to-date Assembly Genome assembly, Read binning, Scaffolding Genome assembly, Read binning, Scaffolding Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/purge_dups /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/purge_dups purge_dups purge_dups Identifying and removing haplotypic duplication in primary genome assemblies | haplotypic duplication identification tool | scripts/pd_config.py: script to generate a configuration file used by run_purge_dups.py | purge haplotigs and overlaps in an assembly based on read depth | Given a primary assembly pri_asm and an alternative assembly hap_asm (optional, if you have one), follow the steps shown below to build your own purge_dups pipeline, steps with same number can be run simultaneously. Among all the steps, although step 4 is optional, we highly recommend our users to do so, because assemblers may produce overrepresented seqeuences. In such a case, The final step 4 can be applied to remove those seqeuences 1 365 365 19303 19303 97 97 1776 1776 80 80 3001 3001 0 0 0 0 24080 24080 542 542 +pycoqc pycoqc html, json QC metrics for ONT Basecalling 2021-03-02 https://github.com/tleonardi/pycoQC 2.5.2 pycoqc 2.5.2 Up-to-date Nanopore Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Sequence analysis, Data quality management, Sequencing Sequence analysis, Data quality management, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pycoqc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pycoqc pycoqc pycoQC PycoQC computes metrics and generates interactive QC plots for Oxford Nanopore technologies sequencing data. 1 832 832 23549 23549 1182 1182 4440 4440 606 606 1143 1143 158 158 322 322 29454 29454 2778 2778 +pygenometracks pygenomeTracks png pyGenomeTracks: Standalone program and library to plot beautiful genome browser tracks. 2018-06-08 https://github.com/deeptools/pyGenomeTracks 3.9 pygenometracks 3.9 Up-to-date Visualization Visualisation, Formatting Visualisation, Formatting Model organisms, Imaging, Workflows Model organisms, Imaging, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pygenometracks /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pygenometracks pygenometracks pyGenomeTracks reproducible plots for multivariate genomic data sets.Standalone program and library to plot beautiful genome browser tracks.pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable. Currently, it is possible to plot:. 1 1301 1446 13377 16146 1427 1472 11997 12438 210 210 5014 5054 44 44 81 81 33719 30469 3172 2982 +pysradb_search pysradb_search tsv, txt pysradb allows to retrieve metadata, such as run accession numbers, from SRA and ENA based on multiple criteria. 2022-11-11 https://github.com/saketkc/pysradb 2.5.1 pysradb 2.5.1 Up-to-date Sequence Analysis Deposition, Data retrieval Deposition, Data retrieval Sequencing, Gene transcripts, Bioinformatics Sequencing, Gene transcripts, Bioinformatics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pysradb /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pysradb pysradb pysradb Python package to query next-generation sequencing metadata and data from NCBI Sequence Read Archive. 1 44 44 178 178 0 0 0 0 0 0 0 0 0 0 0 0 178 178 44 44 +qfilt qfilt fasta Filter sequencing data 2018-06-06 https://github.com/veg/qfilt 1.0.0 qfilt 0.0.1 To update Fastq Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qfilt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qfilt 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +qiime qiime_align_seqs, qiime_alpha_diversity, qiime_alpha_rarefaction, qiime_assign_taxonomy, qiime_beta_diversity, qiime_beta_diversity_through_plots, qiime_compare_categories, qiime_core_diversity, qiime_count_seqs, qiime_extract_barcodes, qiime_filter_alignment, qiime_filter_fasta, qiime_filter_otus_from_otu_table, qiime_filter_samples_from_otu_table, qiime_filter_taxa_from_otu_table, qiime_jackknifed_beta_diversity, qiime_make_emperor, qiime_make_otu_heatmap, qiime_make_phylogeny, qiime_multiple_join_paired_ends, qiime_multiple_split_libraries_fastq, qiime_pick_closed_reference_otus, qiime_pick_open_reference_otus, qiime_pick_otus, qiime_pick_rep_set, qiime_plot_taxa_summary, qiime_split_libraries, qiime_split_libraries_fastq, qiime_summarize_taxa, qiime_summarize_taxa_through_plots, qiime_upgma_cluster, qiime_validate_mapping_file fasta, txt, tabular, html, pdf, fastq, biom1, png, svg, nhx, qual QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org @WRAPPER_VERSION@.0 qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_core /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qiime/qiime_core qiime_core qiime_core QIIME 2™ is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 32 418 483 34279 42817 1 1 1617 1617 1 1 2 16 17 17 4517 4550 49000 40415 502 437 +qiime qiime_collapse_samples, qiime_make_otu_table biom1, tabular QIIME to perform microbial community analysis 2017-01-16 http://www.qiime.org @WRAPPER_VERSION@.0 qiime 1.9.1 To update Metagenomics Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Demultiplexing, Visualisation, Taxonomic classification, Phylogenetic analysis, Sequencing quality control Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics Microbial ecology, Phylogeny, Metagenomics, Metatranscriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime/qiime_add_on /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qiime/qiime_add_on qiime_add_on qiime_add_on QIIME 2 is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed. 2 183 242 2193 2749 0 0 0 0 1 1 2 2 9 9 18 18 2769 2213 252 193 +qiime_extract_viz qiime_extract_viz html Extract vizualization from QIIME artifacts 2022-10-06 http://www.qiime.org @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ unzip To update Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qiime_extract_viz /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qiime_extract_viz 1 31 31 277 277 0 0 0 0 9 9 186 186 0 0 0 0 463 463 40 40 +qq_tools qq_manhattan pdf 2020-10-07 https://CRAN.R-project.org/package=qqman 0.1.0 r-qqman 0.1.4 To update Visualization, Variant Analysis iuc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qq_tools 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 35 35 35 35 1 1 +qualifilter qualifilter tsv, csv, txt Extracts and summarizes QC metrics from MultiQC tabular output to produce a clean, threshold-based QC matrix. 2025-12-15 https://github.com/galaxyproject/tools-iuc 1.0.0 qualifilter 1.0.0 Up-to-date Sequence Analysis, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualifilter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qualifilter 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +qualimap qualimap_bamqc, qualimap_counts, qualimap_multi_bamqc, qualimap_rnaseq html, tsv Qualimap 2 is a platform-independent application written in Java andR that facilitates the quality control of alignment sequencing data and itsderivatives like feature counts. 2019-10-10 http://qualimap.bioinfo.cipf.es/ 2.3 qualimap 2.3 Up-to-date Sequence Analysis, Transcriptomics, SAM Sequencing quality control Sequencing quality control Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/qualimap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/qualimap qualimap QualiMap Platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. 4 2949 3172 735774 740034 3586 3810 117198 120922 847 882 36259 41650 70 70 6924 6924 909530 896155 7934 7452 +quast quast tabular, html, pdf, txt, png Quast (Quality ASsessment Tool) evaluates genome assemblies. 2016-09-07 http://quast.bioinf.spbau.ru/ 5.3.0 quast 5.3.0 Up-to-date Assembly Visualisation, Sequence assembly validation Visualisation, Sequence assembly validation Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quast /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/quast quast QUAST QUAST stands for QUality ASsessment Tool. It evaluates a quality of genome assemblies by computing various metrics and providing nice reports. https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3, https://workflowhub.eu/workflows/403?version=9 microbiome/metagenomics-assembly 1 11028 11672 120605 126603 13078 14773 78457 86986 4849 5353 46644 50987 613 619 14902 14963 279539 260608 32417 29568 +query_impc query_impc tabular Contains a tool to query the IMPC database. 2023-10-11 https://github.com/INFRAFRONTIERDIB/tools-iuc/tree/query_impc/tools/query_impc 0.9.0 requests To update Convert Formats, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_impc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/query_impc 1 2 2 4 4 0 0 0 0 0 0 0 0 0 0 0 0 4 4 2 2 +query_tabular filter_tabular, query_tabular, sqlite_to_tabular tabular, sqlite Loads tabular files into a SQLite DB to perform a SQL query producing a tabular output 2017-07-14 https://github.com/galaxyproject/tools-iuc/tree/master/tools/query_tabular 3.3.1 python To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/query_tabular /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/query_tabular https://usegalaxy.eu/published/workflow?id=3dcf09e75d707573, https://usegalaxy.eu/published/workflow?id=71816adecac46e74, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=cd675ab32d3e7833, https://usegalaxy.eu/published/workflow?id=cefc49c13ff73231, https://workflowhub.eu/workflows/1208?version=1, https://workflowhub.eu/workflows/1218?version=1, https://workflowhub.eu/workflows/403?version=9 microbiome/metagenomics-assembly 3 869 887 150015 159379 898 898 14092 14092 149 149 7881 7895 5 6 96 98 181464 172084 1940 1921 +quickmerge quickmerge fasta, tabular Merge long-read and hybrid assemblies to increase contiguity 2022-07-08 https://github.com/mahulchak/quickmerge @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ quickmerge 0.3 To update Assembly Genome assembly, Scaffolding, De-novo assembly, Genotyping Genome assembly, Scaffolding, De-novo assembly, Genotyping Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype Structural variation, Sequence assembly, DNA polymorphism, Whole genome sequencing, Genotype and phenotype iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quickmerge /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/quickmerge quickmerge quickmerge Quickmerge is a program that uses complementary information from genomes assembled with long reads in order to improve contiguity, and works with assemblies derived from both Pacific Biosciences or Oxford Nanopore. Quickmerge will even work with hybrid assemblies made by combining long reads and Illumina short reads. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +quicktree quicktree newick neighbour-joining phylogenetic inference 2024-11-21 https://github.com/khowe/quicktree @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ quicktree 2.5 To update Phylogenetics Phylogenetic inference (from molecular sequences) Phylogenetic inference (from molecular sequences) Phylogenetics Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/quicktree /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/quicktree quicktree QuickTree QuickTree is an efficient implementation of the Neighbor-Joining algorithm (PMID: 3447015), capable of reconstructing phylogenies from huge alignments in time less than the age of the universe. 1 69 69 466 466 0 0 0 0 0 0 0 0 0 0 0 0 466 466 69 69 +raceid raceid_clustering, raceid_filtnormconf, raceid_inspectclusters, raceid_inspecttrajectory, raceid_trajectory pdf, rds, tabular, txt RaceID3, StemID2, FateID - scRNA analysis 2018-03-03 https://github.com/dgrun/RaceID3_StemID2_package/ 0.4.2 r-raceid 0.1.3 To update Single Cell, Transcriptomics Expression profile clustering, Expression analysis, Molecular dynamics Expression profile clustering, Expression analysis, Molecular dynamics Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression Cell biology, Molecular interactions, pathways and networks, RNA-Seq, Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raceid /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/raceid RaceID RaceID Identification of Cell Types, Inference of Lineage Trees, and Prediction of Noise Dynamics from Single-Cell RNA-Seq Data 5 85 164 973 4613 433 438 3133 3209 4 5 2567 2969 1 1 1 1 10792 6674 608 523 +ragtag ragtag paf, agp, fasta, txt, tabular Reference-guided scaffolding of draft genomes tool. 2021-11-11 https://github.com/malonge/RagTag 2.1.0 ragtag 2.1.0 Up-to-date Assembly Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ragtag /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ragtag ragtag ragtag RagTag is a collection of software tools for scaffolding and improving modern genome assemblies. 1 774 774 8106 8106 6 6 59 59 108 108 2145 2145 32 32 416 416 10726 10726 920 920 +rapidnj rapidnj nhx Galaxy wrapper for the RapidNJ tool 2020-05-11 https://birc.au.dk/software/rapidnj/ @VERSION@ rapidnj 2.3.3 To update Phylogenetics Phylogenetic tree generation Phylogeny Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rapidnj /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rapidnj rapidnj RapidNJ A tool for fast canonical neighbor-joining tree construction. https://usegalaxy.eu/published/workflow?id=a2c46deea34d9d80 1 57 57 3022 3022 285 303 1941 2185 31 31 291 291 13 13 44 44 5542 5298 404 386 +rasusa rasusa bam Randomly subsample sequencing reads to a specified coverage 2024-02-16 https://github.com/mbhall88/rasusa @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rasusa 4.1.0 To update Sequence Analysis Sequence assembly validation, Sequencing quality control Sequence assembly validation Genomics, Sequence analysis, Sequence assembly, Sequencing, RNA-Seq Genomics, Sequence analysis, Sequence assembly, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rasusa /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rasusa rasusa rasusa Rasusa: Randomly subsample sequencing reads to aspecified coverageProduces an unbiased subsample of your reads 1 24 24 104 104 0 0 0 0 0 0 0 0 0 0 0 0 104 104 24 24 +raven raven gfa1, fasta Raven is a de novo genome assembler for long uncorrected reads. 2020-11-04 https://github.com/lbcb-sci/raven 1.8.3 raven-assembler 1.8.3 Up-to-date Assembly De-novo assembly, Genome assembly, Read pre-processing De-novo assembly, Genome assembly, Read pre-processing Sequence assembly, Whole genome sequencing, Genomics Sequence assembly, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raven /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/raven raven Raven a de novo genome assembler for long reads.Raven is a de novo genome assembler for long uncorrected reads. 1 610 610 15837 15837 0 0 0 0 276 276 13041 13041 24 24 217 217 29095 29095 910 910 +raxml raxml txt, nhx RAxML - A Maximum Likelihood based phylogenetic inference 2015-11-05 http://www.exelixis-lab.org/web/software/raxml/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ raxml 8.2.13 To update Phylogenetics Sequence analysis, Phylogenetic tree analysis Sequence analysis Phylogenetics, Sequence analysis Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxml /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/raxml raxml RAxML A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. 1 1422 1464 15492 16986 1144 1144 19599 19633 731 1034 5870 7945 21 21 305 305 44869 41266 3663 3318 +raxmlng raxmlng txt, nhx, json RAxML-NG - A Maximum Likelihood based phylogenetic tree inference 2025-12-20 http://www.exelixis-lab.org/web/software/raxml-ng/ 2.0.2 raxml-ng 2.0.2 Up-to-date Phylogenetics Phylogenetic tree generation (maximum likelihood and Bayesian methods), Phylogenetic tree bootstrapping Phylogenetic tree bootstrapping Phylogenetics, Agricultural science, Phylogenomics Phylogenetics, Agricultural science, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/raxmlng /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/raxmlng RAxML-NG RAxML-NG Phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rcorrector rcorrector fastq Rcorrector (RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. 2018-05-02 https://github.com/mourisl/Rcorrector 1.0.3 rcorrector 1.0.7 To update Fastq Manipulation Sequencing error detection Sequencing error detection RNA, RNA-Seq, Sequencing RNA, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rcorrector /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rcorrector rcorrector Rcorrector This is a kmer-based error correction method for RNA-seq data. It can also be applied to other types of sequencing data where the read coverage is non-uniform, such as single-cell sequencing. 1 78 78 803 803 0 0 0 0 0 0 0 0 0 0 0 0 803 803 78 78 +read2tree read2tree newick Infer a species tree from sequencing reads. 2025-11-23 https://github.com/DessimozLab/read2tree @TOOL_VERSION@ read2tree 2.0.1 To update Phylogenetics Phylogenomics Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read2tree /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/read2tree read2tree read2tree read2tree is a software tool for generating alignment matrices and performing tree inference directly from sequencing reads. It leverages the OMA database and a set of input reads, bypassing many of the standard steps typically required in phylogenomic analysis. In particular, it avoids for read filtering, assembly, gene prediction, gene annotation, all-vs-all comparison, orthology prediction, alignment, and concatenation. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +read_it_and_keep read_it_and_keep Rapid decontamination of SARS-CoV-2 sequencing reads 2022-01-28 https://github.com/GenomePathogenAnalysisService/read-it-and-keep @TOOL_VERSION@ read-it-and-keep 0.3.0 To update Sequence Analysis Filtering, Genome alignment Filtering, Genome alignment Pathology, Genomics Pathology, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/read_it_and_keep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/read_it_and_keep read_it_and_keep read_it_and_keep Read-it-and-keep is a bioinformatics tool designed to filter and extract sequencing reads according to user-defined criteria, such as the presence of specific motifs or coverage of regions of interest. This type of filtering can be particularly useful for targeted analyses, where only relevant sequences are retained for further study, optimising computing and storage resources. 1 81 81 3781 3781 8 8 9 9 0 0 0 0 0 0 0 0 3790 3790 89 89 +recentrifuge recentrifuge html, txt, tabular, xlsx """With Recentrifuge, researchers can analyze results from taxonomic classifiers using interactive charts with emphasis on the confidence level of the classifications.In addition to contamination-subtracted samples.Recentrifuge provides shared and exclusive taxa per sample,thus enabling robust contamination removal and comparative analysis in environmental and clinical metagenomics.""" 2022-05-04 https://github.com/khyox/recentrifuge 1.16.1 recentrifuge 2.1.1 To update Metagenomics Taxonomic classification, Expression analysis, Cross-assembly Taxonomic classification, Expression analysis, Cross-assembly Metagenomics, Microbial ecology, Metagenomic sequencing Metagenomics, Microbial ecology, Metagenomic sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/recentrifuge /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/recentrifuge Recentrifuge Recentrifuge Robust comparative analysis and contamination removal for metagenomics. https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=c09159d7aad0f264 1 306 306 2546 2546 160 160 593 593 37 37 105 105 27 27 2397 2397 5641 5641 530 530 +recount3 recount3 tabular Retrieve harmonized RNA-seq gene expression data from recount3 2026-06-05 https://github.com/LieberInstitute/recount3 @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ bioconductor-recount3 1.20.0 To update Data Source, Transcriptomics RNA-Seq quantification, Statistical calculation RNA-Seq quantification, Statistical calculation Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/recount3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/recount3 recount RECOUNT Probabilistic tag count error correction for next generation sequencing data (Solexa/Illumina). 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +red red fasta, bed Red (REpeat Detector) 2022-09-14 https://github.com/BioinformaticsToolsmith/Red @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ red 2018.09.10 To update Sequence Analysis RNA-Seq analysis, Editing RNA-Seq analysis, Editing RNA, Sequencing, Data visualisation RNA, Sequencing, Data visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/red /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/red red RED This is a program to detect and visualize RNA editing events at genomic scale using next-generation sequencing data. 1 362 362 1237 1237 277 277 556 556 86 86 369 369 60 60 177 177 2339 2339 785 785 +regex_switch regex_switch Regex switch 2025-10-09 https://github.com/galaxyproject/tools-iuc/tree/main/tools/regex_switch @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/regex_switch /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/regex_switch 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +remove_terminal_stop_codons remove_terminal_stop_codons fasta Remove terminal stop codons from coding sequences 2025-12-04 https://github.com/veg/CAPHEINE @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ biopython 1.70 To update Phylogenetics, Sequence Analysis, Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/remove_terminal_stop_codons /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/remove_terminal_stop_codons 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +repeat_masker repeatmasker_wrapper fasta, tabular, txt, gff RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. 2018-04-21 http://www.repeatmasker.org/ 4.1.5 repeatmasker 4.2.4 To update Sequence Analysis Genome annotation Genome annotation Sequence analysis, Sequence composition, complexity and repeats Sequence composition, complexity and repeats bgruening https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmasker /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/repeatmasker repeatmasker RepeatMasker A program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). 1 1428 1448 10157 10293 1181 1219 9955 10202 413 413 4594 4594 91 91 610 610 25699 25316 3171 3113 +repeatmodeler repeatmodeler fasta, stockholm RepeatModeler - Model repetitive DNA 2021-08-26 https://www.repeatmasker.org/RepeatModeler/ 2.0.5 To update Genome annotation Repeat sequence detection Repeat sequence detection Sequence composition, complexity and repeats, Sequence composition, complexity and repeats Sequence composition, complexity and repeats, Sequence composition, complexity and repeats csbl https://github.com/galaxyproject/tools-iuc/tree/main/tools/repeatmodeler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/repeatmodeler repeatmodeler RepeatModeler De-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build, refine and classify consensus models of putative interspersed repeats. 1 725 725 9423 9423 424 424 2473 2473 240 240 8995 8995 30 30 270 270 21161 21161 1419 1419 +repmatch_gff3 repmatch_gff3 tabular, pdf, gff Contains a tool that matches corresponding peak-pair midpoints from separate datasets based onuser-defined criteria. 2015-12-18 @WRAPPER_VERSION@.3 matplotlib To update ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/repmatch_gff3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/repmatch_gff3 1 0 0 0 0 96 224 254 727 0 0 0 0 0 0 0 0 727 254 224 96 +reshape2 cast, melt tabular Flexibly restructure and aggregate data using just the two functions melt and dcast 2017-05-26 https://cran.r-project.org/web/packages/reshape2/index.html 1.4.2 r-reshape2 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/reshape2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/reshape2 2 112 123 3506 3687 100 131 421 585 0 0 0 0 3 3 6 6 4278 3933 257 215 +resize_coordinate_window resize_coordinate_window gff Contains a tool that modifies the start and stop coordinates of GFF data, expanding the coordinate windowby a specified size. 2016-01-13 1.0.2 python To update Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/resize_coordinate_window /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/resize_coordinate_window 1 6 9 13 86 22 60 36 221 0 0 0 0 0 0 0 0 307 49 69 28 +revoluzer revoluzer_crex, revoluzer_distmat tabular revoluzer wrappers 2024-03-19 https://gitlab.com/Bernt/revoluzer/ 0.1.8 revoluzer 0.1.8 Up-to-date Phylogenetics Structural variation detection Structural variation detection Molecular evolution, Phylogeny Molecular evolution, Phylogeny iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/revoluzer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/revoluzer revoluzer revoluzer Various tools for genome rearrangement analysis. CREx, TreeREx, etc 2 68 68 3932 3932 0 0 0 0 0 0 0 0 0 0 0 0 3932 3932 68 68 +rgcca rgcca pdf, tsv, rdata multi-block analysis 2020-09-02 https://github.com/rgcca-factory/RGCCA 3.0.2 rgccacmd 3.0.3 To update Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgcca /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rgcca 1 7 7 46 46 40 40 94 94 0 0 0 0 0 0 0 0 140 140 47 47 +rgrnastar rna_star, rna_starsolo txt, interval, bam, unsorted.bam, tabular, tsv, mtx RNA STAR is an ultra fast universal RNA and scRNA-seq aligner and mapper 2015-05-18 https://github.com/alexdobin/STAR 2.7.11b star 2.7.11b Up-to-date Next Gen Mappers, Transcriptomics, Single Cell Sequence alignment Sequence alignment RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rgrnastar /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rgrnastar star STAR Ultrafast universal RNA-seq data aligner https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765, https://usegalaxy.eu/published/workflow?id=deec04097a871646 2 11597 13300 454740 555235 17153 22174 406678 513360 1461 1710 55618 62678 1016 1019 12202 12241 1143514 929238 38203 31227 +ribowaltz ribowaltz_process, ribowaltz_plot tabular, rdata Calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data 2022-09-22 https://github.com/LabTranslationalArchitectomics/riboWaltz 1.2.0 ribowaltz 2.0 To update Transcriptomics, RNA Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ribowaltz /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ribowaltz riboWaltz riboWaltz riboWaltz is an R package for calculation of optimal P-site offsets, diagnostic analysis and visual inspection of ribosome profiling data. 2 21 21 204 204 0 0 0 0 0 0 0 0 0 0 0 0 204 204 21 21 +rmlst_cli rmlst_cli json Identify bacterial species using the PubMLST rMLST API. 2026-06-16 https://github.com/ssi-dk/rmlst-cli 1.1 rmlst-cli 1.1 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rmlst_cli /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rmlst_cli 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rnaquast rna_quast txt, tgz, pdf, tabular rnaQuast (RNA Quality Assessment Tool) evaluates genome assemblies. 2020-10-05 https://github.com/ablab/rnaquast 2.3.2 rnaquast 2.3.2 Up-to-date Assembly, RNA De-novo assembly, Transcriptome assembly, Sequence assembly validation De-novo assembly, Transcriptome assembly, Sequence assembly validation Sequence assembly, Transcriptomics, RNA-Seq Sequence assembly, Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rnaquast /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rnaquast rnaQUAST rnaQUAST Quality assessment tool for de novo transcriptome assemblies. 1 375 375 1887 1887 196 196 767 767 31 31 326 326 11 11 103 103 3083 3083 613 613 +roary roary tabular, fasta, csv, nhx, dot, embl, txt Roary the pangenome pipeline 2017-06-21 https://sanger-pathogens.github.io/Roary/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ roary 3.13.0 To update Sequence Analysis Genome assembly Genome assembly DNA, Genomics, Mapping DNA, Genomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/roary /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/roary roary Roary A high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome. 1 2251 2377 21218 23887 2319 2454 17744 18851 653 749 5251 7169 47 47 187 187 50094 44400 5627 5270 +rp2biosensor rp2biosensor html, json Build Sensing-Enabling Metabolic Pathways from RetroPath2.0 output 2023-01-05 https://github.com/brsynth/rp2biosensor @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rp2biosensor To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2biosensor /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rp2biosensor 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rp2paths rp2paths csv, tabular Enumerate and seperate the different pathways generated by RetroPath2.0 2022-10-17 https://github.com/brsynth/rp2paths @TOOL_VERSION@ rp2paths To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rp2paths /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rp2paths 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rpbasicdesign rpbasicdesign csv Extracting enzyme IDs from rpSBML files 2022-03-30 https://github.com/brsynth/rpbasicdesign @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rpbasicdesign To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpbasicdesign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rpbasicdesign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rpfba rpfba sbml Perform FBA for the RetroPath2.0 heterologous pathways 2022-01-17 https://github.com/brsynth/rptools/releases @TOOL_VERSION@ rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rpfba /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rpfba 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rptools rptools_rpextractsink, rptools_rpfba, rptools_rpranker, rptools_rpreport, rptools_rpviz csv, sbml, html Suite of tools that work on rpSBML format 2022-11-16 https://github.com/brsynth/rptools @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rptools To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rptools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rptools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rrmscorer rrmscorer Predicts RNA Recognition Motif (RRM) scores for protein sequences. 2025-09-17 https://bio2byte.be/rrmscorer/ 1.0.11 rrmscorer 1.0.11 Up-to-date Sequence Analysis Multiple sequence alignment, Calculation, Visualisation Multiple sequence alignment, Calculation, Visualisation Computational biology Computational biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrmscorer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rrmscorer RRMScorer RRMScorer RRMScorer provides quick predictions for any RNA recognition motif (RRM) and any RNA target purely based on their sequences. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rrparser rrparser csv Reaction Rules Parser 2022-06-27 https://github.com/brsynth/RRParser @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ rrparser To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/rrparser /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rrparser 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +rseqc rseqc_FPKM_count, rseqc_RNA_fragment_size, rseqc_RPKM_saturation, rseqc_bam2wig, rseqc_bam_stat, rseqc_clipping_profile, rseqc_deletion_profile, rseqc_geneBody_coverage, rseqc_geneBody_coverage2, rseqc_infer_experiment, rseqc_inner_distance, rseqc_insertion_profile, rseqc_junction_annotation, rseqc_junction_saturation, rseqc_mismatch_profile, rseqc_read_GC, rseqc_read_NVC, rseqc_read_distribution, rseqc_read_duplication, rseqc_read_hexamer, rseqc_read_quality, rseqc_tin tabular, wig, txt, pdf an RNA-seq quality control package 2017-02-27 https://code.google.com/p/rseqc/ 5.0.3 rseqc 5.0.4 To update Convert Formats, Sequence Analysis, RNA, Transcriptomics, Visualization Data handling Data handling Sequencing Sequencing nilesh https://github.com/galaxyproject/tools-iuc/tree/main/tools/rseqc /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/rseqc rseqc RSeQC Provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 22 4113 5223 155237 181534 4079 5016 146353 197501 629 697 28108 32069 809 810 78294 78366 489470 407992 11746 9630 +ruvseq ruvseq pdf Remove Unwanted Variation from RNA-Seq Data 2018-08-30 https://www.bioconductor.org/packages/release/bioc/html/DESeq2.html @TOOL_VERSION@+galaxy@WRAPPER_VERSION@ bioconductor-ruvseq 1.44.0 To update Transcriptomics, RNA, Statistics Differential gene expression analysis Differential gene expression analysis Gene expression, RNA-seq Gene expression iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ruvseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ruvseq ruvseq RUVSeq This package implements the remove unwanted variation (RUV) methods for the normalization of RNA-Seq read counts between samples. 1 155 200 1182 1507 272 319 2100 2428 0 0 0 0 0 0 0 0 3935 3282 519 427 +salsa salsa fasta, agp A tool to scaffold long read assemblies with Hi-C 2021-01-14 https://github.com/marbl/SALSA @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ salsa2 2.3 To update Assembly Genome assembly, De-novo assembly, Scaffolding Genome assembly, De-novo assembly, Scaffolding Sequence assembly, DNA binding sites, Mapping Sequence assembly, DNA binding sites, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/salsa2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/salsa2 SALSA SALSA > VERY_LOW CONFIDENCE! | > CORRECT NAME OF TOOL COULD ALSO BE 'chromosome-scale', 'reference-quality', 'Hi-C', 'scaffolder' | Integrating Hi-C links with assembly graphs for chromosome-scale assembly | SALSA: A tool to scaffold long read assemblies with Hi-C data | SALSA: A tool to scaffold long read assemblies with Hi-C | This code is used to scaffold your assemblies using Hi-C data. This version implements some improvements in the original SALSA algorithm. If you want to use the old version, it can be found in the old_salsa branch 1 130 130 495 495 103 103 1074 1074 24 24 410 410 0 0 0 0 1979 1979 257 257 +samblaster samblaster bam, fastqsanger samblaster marks duplicates and can output split and discordant alignments from SAM/BAM files 2016-12-18 https://github.com/GregoryFaust/samblaster @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ samblaster 0.1.26 To update SAM, Fastq Manipulation, Variant Analysis Split read mapping Split read mapping DNA, Sequencing, Mapping DNA, Sequencing, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/samblaster /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/samblaster samblaster SAMBLASTER A tool to mark duplicates and extract discordant and split reads from SAM files. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +samestr samestr_compare, samestr_convert, samestr_extract, samestr_filter, samestr_merge, samestr_stats, samestr_summarize tabular, fasta, fasta.gz, npz Strain-level analysis and comparison of metagenomic samples 2026-04-15 https://github.com/danielpodlesny/samestr 1.2025.111 samestr 1.2025.111 Up-to-date Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/samestr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/samestr 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +samtools 2017-01-24 https://github.com/samtools/samtools 1.22 samtools 1.23.1 To update SAM iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/samtools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/samtools 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +sansa sansa_annotate bcf, tabular.gz, txt Sansa is a tool for structural variant annotation. 2020-12-05 https://github.com/dellytools/sansa 0.2.5 sansa 0.2.5 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sansa /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sansa 1 43 43 157 157 0 0 0 0 0 0 0 0 0 0 0 0 157 157 43 43 +sarscov2formatter sarscov2formatter fasta, json sarscov2formatter custom script 2020-05-01 https://github.com/nickeener/sarscov2formatter @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ sarscov2formatter 1.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2formatter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sarscov2formatter 1 14 16 40 174 26 30 48 402 0 0 0 0 0 0 0 0 576 88 46 40 +sarscov2summary sarscov2summary json sarscov2summary custom script 2020-05-01 https://github.com/nickeener/sarscov2summary 0.1 sarscov2summary 0.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sarscov2summary /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sarscov2summary 1 3 5 3 140 3 6 4 253 0 0 0 0 0 0 0 0 393 7 11 6 +sbml2sbol sbml2sbol xml Convert SBML to SBOL format 2022-10-15 https://github.com/neilswainston/SbmlToSbol @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ sbml2sbol To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sbml2sbol /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sbml2sbol 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +scanpy scanpy_cluster_reduce_dimension, scanpy_filter, scanpy_inspect, scanpy_normalize, scanpy_plot, scanpy_remove_confounders tabular, png, pdf, svg, txt, h5ad, vitessce.json, json Scanpy – Single-Cell Analysis in Python 2019-03-04 https://scanpy.readthedocs.io 1.11.5 scanpy 1.7.2 To update Single Cell, Spatial Omics, Transcriptomics Differential gene expression analysis, Principal component visualisation, Expression profile clustering Differential gene expression analysis, Principal component visualisation, Expression profile clustering Gene expression, Cell biology, Genetics, Single-cell sequencing Gene expression, Cell biology, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scanpy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scanpy scanpy SCANPY Scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. 6 771 868 70187 77433 456 465 42066 42163 120 121 22195 23258 2 2 114 114 142968 134562 1456 1349 +scater scater_create_qcmetric_ready_sce, scater_filter, scater_plot_dist_scatter, scater_plot_pca, scater_plot_tsne loom, pdf Scater (Single-Cell Analysis Toolkit for gene Expression data in R) is acollection of tools for doing various analyses of single-cell RNA-seq geneexpression data, with a focus on quality control and visualization. 2019-07-18 http://bioconductor.org/packages/scater/ 1.22.0 bioconductor-scater 1.38.0 To update Single Cell, Transcriptomics, Visualization Read pre-processing, Sequencing quality control, Sequence visualisation Read pre-processing, Sequence visualisation RNA-Seq, Quality affairs, Molecular genetics RNA-Seq, Quality affairs, Molecular genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scater /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scater scater scater Pre-processing, quality control, normalization and visualization of single-cell RNA-seq data. 5 77 94 1007 1409 0 0 0 0 7 8 1094 1215 0 0 0 0 2624 2101 102 84 +sceasy_convert sceasy_convert rdata, h5, h5ad Converter between difference single-cell formats 2023-11-10 https://github.com/cellgeni/sceasy/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-sceasy 0.0.7 To update Single Cell, Spatial Omics, Convert Formats Data handling Data handling iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sceasy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sceasy sceasy sceasy sceasy is a package that helps easy conversion of different single-cell data formats to each other. 1 301 310 1543 1615 103 104 521 522 5 5 349 349 1 1 2 2 2488 2415 420 410 +schicexplorer schicexplorer_schicadjustmatrix, schicexplorer_schiccluster, schicexplorer_schicclustercompartments, schicexplorer_schicclusterminhash, schicexplorer_schicclustersvl, schicexplorer_schicconsensusmatrices, schicexplorer_schiccorrectmatrices, schicexplorer_schiccreatebulkmatrix, schicexplorer_schicdemultiplex, schicexplorer_schicinfo, schicexplorer_schicmergematrixbins, schicexplorer_schicmergetoscool, schicexplorer_schicnormalize, schicexplorer_schicplotclusterprofiles, schicexplorer_schicplotconsensusmatrices, schicexplorer_schicqualitycontrol scool, txt, png scHiCExplorer: Set of programs to process, analyze and visualize scHi-C data. 2019-12-16 https://github.com/joachimwolff/schicexplorer 4 schicexplorer 7 To update Sequence Analysis, Transcriptomics, Visualization, Single Cell Validation, Visualisation, Standardisation and normalisation Validation, Visualisation, Standardisation and normalisation Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics Workflows, DNA, Chromosome conformation capture, ChIP-seq, Epigenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/schicexplorer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/schicexplorer hicexplorer HiCExplorer A web server for reproducible Hi-C, capture Hi-C and single-cell Hi-C data analysis, quality control and visualization.HiCExplorer — HiCExplorer 3.6 documentation.scHiCExplorer — scHiCExplorer 7 documentation.Free document hosting provided by Read the Docs. 16 8 11 99 821 12 12 32 32 2 2 1351 1351 0 0 0 0 2204 1482 25 22 +scikit_bio scikit_bio_diversity_beta_diversity tabular scikit-bio: an open-source, BSD-licensed, python package providing data structures, algorithms, and educational resources for bioinformatics 2016-05-31 http://scikit-bio.org/ 0.4.2 scikit-bio 0.4.2 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scikit-bio /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scikit-bio 1 1 1 1 1 303 445 1472 2106 0 0 0 0 0 0 0 0 2107 1473 446 304 +scoary scoary tabular, newick Scoary calculates the assocations between all genes in the accessory genome and the traits. 2021-03-18 https://github.com/AdmiralenOla/Scoary @TOOL_VERSION@ scoary 1.6.16 To update Metagenomics Analysis Analysis Genotype and phenotype, Model organisms, GWAS study, Functional genomics Genotype and phenotype, Model organisms, GWAS study, Functional genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scoary /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scoary scoary Scoary Pan-genome wide association studies and is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome (all genes that are present in i genomes where 1 < i < N) and the traits. It reports a list of genes sorted by strength of association per trait. 1 113 113 1366 1366 0 0 0 0 0 0 0 0 0 0 0 0 1366 1366 113 113 +scop3p scop3p tabular, json Fetch post-translational modifications (PTMs) from Scop3P database 2026-02-06 https://iomics.ugent.be/scop3p/index 1.1.0 scop3p 1.1.0 Up-to-date Proteomics, Data Source iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scop3p /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scop3p 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +scpipe scpipe tabular, pdf, html, txt, rdata A flexible preprocessing pipeline for single-cell RNA-sequencing data 2018-08-12 http://bioconductor.org/packages/release/bioc/html/scPipe.html 1.0.0 bioconductor-scpipe 2.10.0 To update Transcriptomics, Single Cell Genome annotation, Validation, Alignment, Visualisation Genome annotation, Validation, Alignment, Visualisation Gene expression, RNA-Seq, Sequencing Gene expression, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/scpipe /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/scpipe scpipe scPipe A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols. 1 25 40 149 643 50 63 656 799 1 1 1 1 0 0 0 0 1443 806 104 76 +seaborn seaborn, seaborn_pairgrid png Seaborn is a Python data visualization library based on Matplotlib. 2025-05-13 https://seaborn.pydata.org/ 0.13.2 seaborn To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seaborn /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seaborn 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +seacr seacr tabular SEACR is intended to call peaks and enriched regions from sparse CUT&RUN or chromatin profiling data in which background is dominated by zeroes. 2020-02-05 https://github.com/FredHutch/SEACR @TOOL_VERSION@+@WRAPPER_VERSION@ seacr 1.3 To update Epigenetics, ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seacr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seacr 1 150 155 6871 7014 289 289 8117 8117 0 0 0 0 0 0 0 0 15131 14988 444 439 +selenzy_wrapper selenzy_wrapper sbml, csv Performs enzyme selection from a reaction query. 2022-06-29 https://github.com/brsynth/selenzy-wrapper @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ selenzy_wrapper 0.3.1 To update Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/selenzy_wrapper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/selenzy_wrapper 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +semibin semibin_bin, semibin_concatenate_fasta, semibin_generate_cannot_links, semibin_generate_sequence_features, semibin, semibin_train fasta, csv SemiBin: Semi-supervised Metagenomic Binning Using Siamese Neural Networks 2022-10-14 https://semibin.readthedocs.io/en/latest/ 2.1.0 semibin 2.3.0 To update Metagenomics Sequence assembly, Read binning Sequence assembly, Read binning Metagenomics, Machine learning, Microbial ecology, Sequence assembly Metagenomics, Machine learning, Microbial ecology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/semibin /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/semibin semibin SemiBin Command tool for metagenomic binning with semi-supervised deep learning using information from reference genomes. 6 53 53 2779 2779 9 9 18 18 0 0 0 0 2 2 75 75 2872 2872 64 64 +seq2hla seq2hla txt, tabular Precision HLA typing and expression from RNAseq data 2020-02-20 https://github.com/TRON-Bioinformatics/seq2HLA @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ seq2hla 2.3 To update Sequence Analysis Read mapping, Genetic variation analysis Read mapping, Genetic variation analysis Transcriptomics, Mapping Transcriptomics, Mapping iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seq2hla /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seq2hla seq2hla Seq2HLA seq2HLA is a computational tool to determine Human Leukocyte Antigen (HLA) directly from existing and future short RNA-Seq reads. It takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising known HLA alleles and outputs the most likely HLA class I and class II types, a p-value for each call, and the expression of each class. 1 62 65 432 482 11 11 49 49 6 6 102 102 0 0 0 0 633 583 82 79 +seqcomplexity seqcomplexity json Sequence complexity for raw reads 2022-06-07 https://github.com/stevenweaver/seqcomplexity @TOOL_VERSION@ seqcomplexity 0.1.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqcomplexity /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqcomplexity 1 25 25 84 84 55 55 133 133 0 0 0 0 0 0 0 0 217 217 80 80 +seqkit seqkit_fx2tab, seqkit_grep, seqkit_head, seqkit_locate, seqkit_sort, seqkit_split2, seqkit_stats, seqkit_translate tabular, txt A cross-platform and ultrafast toolkit for FASTA/Q file manipulation 2022-06-01 https://bioinf.shenwei.me/seqkit/ 2.13.0 seqkit 2.13.0 Up-to-date Sequence Analysis DNA transcription, Sequence trimming, DNA translation, Sequence conversion DNA transcription, Sequence trimming, DNA translation Database management, Sequence analysis Database management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqkit seqkit seqkit FASTA and FASTQ are basic and ubiquitous formats for storing nucleotide and protein sequences. Common manipulations of FASTA/Q file include converting, searching, filtering, deduplication, splitting, shuffling, and sampling. Existing tools only implement some of these manipulations, and not particularly efficiently, and some are only available for certain operating systems. Furthermore, the complicated installation process of required packages and running environments can render these programs less user friendly. SeqKit demonstrates competitive performance in execution time and memory usage compared to similar tools. The efficiency and usability of SeqKit enable researchers to rapidly accomplish common FASTA/Q file manipulations. 8 396 396 13926 13926 0 0 0 0 120 120 2190 2190 69 69 648 648 16764 16764 585 585 +seqprep seqprep fastq.gz Tool for merging paired-end Illumina reads and trimming adapters. 2024-01-15 https://github.com/jstjohn/SeqPrep 1.3.2 seqprep 1.3.2 Up-to-date Fastq Manipulation, Sequence Analysis Nucleic acid design Nucleic acid design Genomics, Sequence assembly, Sequencing, Probes and primers Genomics, Sequence assembly, Sequencing, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqprep /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqprep seqprep SeqPrep Strips adapters and optionally merges overlapping paired-end (or paired-end contamination in mate-pair libraries) illumina style reads. 1 227 227 3602 3602 0 0 0 0 0 0 0 0 0 0 0 0 3602 3602 227 227 +seqsero2 seqsero2 tabular, txt Salmonella serotype prediction from genome sequencing data 2023-11-07 https://github.com/denglab/SeqSero2 1.3.2 seqsero2 1.3.2 Up-to-date Sequence Analysis Genome indexing, Antimicrobial resistance prediction, Genome alignment Genome indexing, Antimicrobial resistance prediction, Genome alignment Whole genome sequencing, Sequence assembly, Genomics Whole genome sequencing, Sequence assembly, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqsero2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqsero2 seqsero2 SeqSero2 "rapid and improved Salmonella serotype determination using whole genome sequencing data | SeqSero-Salmonella Serotyping by Whole Genome Sequencing | Salmonella Serotyping by Whole Genome Sequencing | Online version: http://www.denglab.info/SeqSero2 | Salmonella serotype prediction from genome sequencing data | Citation: SeqSero, Zhang et al. 2015; SeqSero2, Zhang et al. 2019 | Salmonella serotype derterminants databases | Upon executing the command, a directory named 'SeqSero_result_Time_your_run' will be created. Your result will be stored in 'SeqSero_result.txt' in that directory. And the assembled alleles can also be found in the directory if using ""-m a"" (allele mode)" 1 116 116 14011 14011 0 0 0 0 0 0 0 0 2 2 2 2 14013 14013 118 118 +seqtk seqtk_comp, seqtk_cutN, seqtk_dropse, seqtk_fqchk, seqtk_hety, seqtk_listhet, seqtk_mergefa, seqtk_mergepe, seqtk_mutfa, seqtk_randbase, seqtk_sample, seqtk_seq, seqtk_subseq, seqtk_telo, seqtk_trimfq tabular, auto, bed Toolkit for processing sequences in FASTA/Q formats 2015-01-13 https://github.com/lh3/seqtk 1.5 seqtk 1.5 Up-to-date Sequence Analysis Data handling, Sequence file editing Data handling, Sequence file editing Data management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqtk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqtk seqtk seqtk A tool for processing sequences in the FASTA or FASTQ format. It parses both FASTA and FASTQ files which can also be optionally compressed by gzip. microbiome/metagenomics-assembly 15 804 862 270417 273634 956 1098 107899 122221 260 262 158312 159084 55 55 18691 18691 573630 555319 2277 2075 +sequali sequali html, json Fast sequencing data quality metrics for short and long reads 2025-03-19 https://sequali.readthedocs.io/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ sequali 1.0.2 To update Fastq Manipulation Sequencing quality control, Statistical calculation Sequencing quality control, Statistical calculation Data quality management, Sequence analysis Data quality management, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sequali /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sequali sequali Sequali Fast sequencing data quality metrics 1 9 9 16 16 0 0 0 0 0 0 0 0 0 0 0 0 16 16 9 9 +seqwish seqwish gfa1 Alignment to variation graph inducer 2020-04-06 https://github.com/ekg/seqwish @TOOL_VERSION@ seqwish 0.7.11 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seqwish /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seqwish 1 0 2 0 271 0 0 0 0 0 0 0 0 0 0 0 0 271 0 2 0 +seurat seurat_create, seurat_data, seurat_integrate, seurat_clustering, seurat_preprocessing, seurat_plot, seurat_reduce_dimension Seurat - R toolkit for single cell genomics 2018-08-20 https://satijalab.org/seurat/ 5.4.0 r-seurat 3.0.2 To update Single Cell, Transcriptomics, Sequence Analysis RNA-Seq, Transcriptomics RNA-Seq, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/seurat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/seurat seurat Seurat Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneity from single-cell transcriptomic measurements, and to integrate diverse types of single-cell data. 7 120 120 6468 6468 109 109 2871 2871 9 9 1332 1332 4 4 105 105 10776 10776 242 242 +sexdeterrmine sexdeterrmine tabular, json Sex.DetERRmine calculates the relative coverage of sex chromosomes to determine biological sex. 2026-03-11 https://github.com/TCLamnidis/Sex.DetERRmine @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ sexdeterrmine 1.1.2 To update Sequence Analysis, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sexdeterrmine /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sexdeterrmine 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +sfold sfold Predict the probable RNA secondary structures through structure ensemble sampling 2024-10-09 https://github.com/Ding-RNA-Lab/Sfold 2.2.0 To update RNA iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sfold /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sfold 1 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 +shasta shasta gfa1, txt, csv, fasta Fast de novo assembly of long read sequencing data 2020-11-11 https://github.com/chanzuckerberg/shasta 0.6.0 shasta 0.14.0 To update Assembly, Nanopore iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shasta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/shasta 1 399 399 1291 1291 0 0 0 0 98 98 791 791 0 0 0 0 2082 2082 497 497 +shorah_amplicon shorah_amplicon tabular, txt Reconstruct haplotypes using ShoRAH in amplicon mode 2018-11-27 https://github.com/cbg-ethz/shorah/blob/master/README.md @VERSION@ shorah 1.99.2 To update Sequence Analysis Haplotype mapping, Variant calling Haplotype mapping, Variant calling Metagenomics, Sequencing, Genetics Metagenomics, Sequencing, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shorah /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/shorah shorah ShoRAH Inference of a population from a set of short reads. The package contains programs that support mapping of reads to a reference genome, correcting sequencing errors by locally clustering reads in small windows of the alignment, reconstructing a minimal set of global haplotypes that explain the reads, and estimating the frequencies of the inferred haplotypes. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +shovill shovill txt, fasta, unsorted.bam, gfa1 Faster de novo assembly pipeline based around Spades 2017-10-24 https://github.com/tseemann/shovill @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ shovill 1.4.2 To update Assembly Genome assembly Genome assembly Genomics, Microbiology, Sequence assembly Genomics, Microbiology, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/shovill /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/shovill shovill shovill Shovill is a pipeline for assembly of bacterial isolate genomes from Illumina paired-end reads. Shovill uses SPAdes at its core, but alters the steps before and after the primary assembly step to get similar results in less time. Shovill also supports other assemblers like SKESA, Velvet and Megahit, so you can take advantage of the pre- and post-processing the Shovill provides with those too. https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3 1 3269 3491 70801 76107 4933 5212 51724 55190 1425 1669 30312 35794 83 83 9136 9136 176227 161973 10455 9710 +sickle sickle txt A windowed adaptive trimming tool for FASTQ files using quality 2015-11-03 https://github.com/najoshi/sickle 1.33.3 sickle-trim 1.33 To update Fastq Manipulation, Sequence Analysis Sequence trimming Sequence trimming Data quality management Data quality management iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sickle /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sickle sickle sickle A tool that uses sliding windows along with quality and length thresholds to determine when quality is sufficiently low to trim the 3'-end of reads and also determines when the quality is sufficiently high enough to trim the 5'-end of reads. 1 627 731 20571 21706 1315 1394 11397 12999 0 0 0 0 147 149 1215 1324 36029 33183 2274 2089 +simpleweather simple_weather html provides simple weather in text format 2016-07-19 http://wttr.in/ 0.1.2 curl To update Visualization, Web Services iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/weather_app /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/weather_app 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +simtext abstracts_by_pmids, pmids_to_pubtator_matrix, pubmed_by_queries, text_to_wordmatrix tabular A text mining framework for interactive analysis and visualization of similarities among biomedical entities. 2021-02-28 https://github.com/dlal-group/simtext 0.0.2 r-argparse 1.0.1 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/simtext /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/simtext 4 32 32 234 234 0 0 0 0 5 5 608 608 0 0 0 0 842 842 37 37 +sina sina fasta, data, tabular, txt SINA reference based multiple sequence alignment 2019-10-11 https://sina.readthedocs.io/en/latest/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ sina 1.7.2 To update Sequence Analysis Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequence alignment analysis, Multiple sequence alignment, Taxonomic classification, Structure-based sequence alignment Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy Sequencing, RNA, Nucleic acid structure analysis, Taxonomy, Sequence analysis, Taxonomy iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sina /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sina sina SINA Aligns and optionally taxonomically classifies your rRNA gene sequences.Reference based multiple sequence alignment 1 123 143 1180 1492 377 460 2041 2558 0 0 0 0 0 0 0 0 4050 3221 603 500 +sinto sinto_barcode, sinto_fragments fastqsanger.gz, bed Sinto single-cell analysis tools 2023-04-12 https://github.com/timoast/sinto 0.10.1 sinto 0.10.1 Up-to-date Single Cell, Epigenetics Bioinformatics, Cell biology Bioinformatics, Cell biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sinto /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sinto sinto sinto Sinto is a toolkit for processing aligned single-cell data. 2 48 48 350 350 28 28 221 221 1 1 190 190 0 0 0 0 761 761 77 77 +slamdunk alleyoop, slamdunk bam, tabular, vcf Slamdunk maps and quantifies SLAMseq reads 2018-10-05 http://t-neumann.github.io/slamdunk 0.4.3 slamdunk 0.4.3 Up-to-date RNA, Transcriptomics, Sequence Analysis, Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/slamdunk /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/slamdunk 2 10 13 159 402 55 57 1312 1380 0 0 0 0 0 0 0 0 1782 1471 70 65 +sleuth sleuth tabular, pdf Sleuth is a program for differential analysis of RNA-Seq data. 2023-05-30 https://github.com/pachterlab/sleuth 0.30.2 r-sleuth 0.30.2 Up-to-date Transcriptomics, RNA, Statistics Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation Expression data visualisation, Differential gene expression analysis, Gene expression profiling, Statistical calculation RNA-Seq, Gene expression, Statistics and probability RNA-Seq, Gene expression, Statistics and probability iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sleuth /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sleuth sleuth sleuth A statistical model and software application for RNA-seq differential expression analysis. 1 42 42 204 204 0 0 0 0 0 0 0 0 0 0 0 0 204 204 42 42 +smallgenomeutilities smgu_frameshift_deletions_checks tabular Set of utilities for manipulating small viral genome data. 2023-05-30 https://github.com/cbg-ethz/smallgenomeutilities 0.5.2 smallgenomeutilities 0.5.2 Up-to-date Sequence Analysis Read pre-processing, Sequence alignment, Genetic variation analysis Read pre-processing, Sequence alignment, Genetic variation analysis Genomics, Population genetics, Workflows, Virology, Sequencing Genomics, Population genetics, Workflows, Virology, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/smallgenomeutilities /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/smallgenomeutilities v-pipe V-pipe Bioinformatics pipeline for the analysis of next-generation sequencing data derived from intra-host viral populations. 1 15 15 168 168 0 0 0 0 0 0 0 0 0 0 0 0 168 168 15 15 +smudgeplot smudgeplot png, tabular, txt Inference of ploidy and heterozygosity structure using whole genome sequencing 2022-07-01 https://github.com/KamilSJaron/smudgeplot 0.2.5 smudgeplot 0.5.3 To update Assembly Sequence trimming, Genotyping, k-mer counting Sequence trimming, Genotyping, k-mer counting Sequence assembly, Genetic variation, Mathematics Sequence assembly, Genetic variation, Mathematics galaxy-australia https://github.com/galaxyproject/tools-iuc/tree/main/tools/smudgeplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/smudgeplot smudgeplots Smudgeplots Reference-free profiling of polyploid genomes | Inference of ploidy and heterozygosity structure using whole genome sequencing data | Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example: | This tool extracts heterozygous kmer pairs from kmer dump files and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovA / (CovA + CovB)). Such an approach also allows us to analyze obscure genomes with duplications, various ploidy levels, etc | GenomeScope 2.0 and Smudgeplots: Reference-free profiling of polyploid genomes Timothy Rhyker Ranallo-Benavidez, Kamil S. Jaron, Michael C. Schatz bioRxiv 747568; doi: https://doi.org/10.1101/747568 https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 1 146 146 805 805 90 90 242 242 78 78 1315 1315 0 0 0 0 2362 2362 314 314 +snap snap, snap_training gff, fasta, snaphmm SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. 2017-10-12 https://github.com/KorfLab/SNAP 2013_11_29 snap 2013_11_29 Up-to-date Sequence Analysis Gene prediction Gene prediction DNA, DNA polymorphism, Genetics DNA polymorphism, Genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snap snap SNAP The Semi-HMM-based Nucleic Acid Parser is a gene prediction tool. 2 348 410 1443 1821 258 292 813 939 100 101 578 594 0 0 0 0 3354 2834 803 706 +snapatac2 snapatac2_clustering, snapatac2_metrics, snapatac2_network, snapatac2_peaks_and_motif, snapatac2_plotting, snapatac2_preprocessing h5ad, txt, tabular, png, pdf, svg, html, interval SnapATAC2 – A Python/Rust package for single-cell epigenomics analysis 2024-05-16 https://kzhang.org/SnapATAC2/ 2.8.0 To update Single Cell, Epigenetics Essential dynamics, Dimensionality reduction, Gene expression profiling Essential dynamics, Dimensionality reduction, Gene expression profiling Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing Epigenomics, Cell biology, Chromosome conformation capture, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snapatac2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snapatac2 snapatac SnapATAC SnapATAC (Single Nucleus Analysis Pipeline for ATAC-seq) is a fast, accurate and comprehensive method for analyzing single cell ATAC-seq datasets. 6 14 14 2521 2521 14 14 65 65 1 1 1633 1633 0 0 0 0 4219 4219 29 29 +sniffles sniffles vcf Galaxy wrapper for sniffles 2020-08-29 https://github.com/fritzsedlazeck/Sniffles @TOOL_VERSION@ sniffles 2.8.0 To update Sequence Analysis Sequence analysis, Structural variation detection Sequence analysis, Structural variation detection DNA structural variation, Sequencing Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sniffles /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sniffles sniffles Sniffles An algorithm for structural variation detection from third generation sequencing alignment. 1 205 205 1813 1813 246 246 1546 1546 98 98 2716 2716 4 4 11 11 6086 6086 553 553 +snipit snipit png, csv Summarise snps relative to a reference sequence 2022-07-17 https://github.com/aineniamh/snipit @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ snipit 1.7 To update Variant Analysis, Sequence Analysis Base position variability plotting Base position variability plotting Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snipit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snipit snipit snipit Summarise snps relative to a reference sequence 1 88 88 1354 1354 16 16 84 84 0 0 0 0 0 0 0 0 1438 1438 104 104 +snippy snippy_core, snippy, snippy_clean_full_aln fasta, tabular, txt, vcf, gff3, bam, zip Contains the snippy tool for characterising microbial snps 2017-07-13 https://github.com/tseemann/snippy @WRAPPER_VERSION@+galaxy@VERSION_SUFFIX@ snippy 4.6.0 To update Sequence Analysis Phylogenetic tree visualisation, Phylogenetic tree generation, Variant calling Phylogenetic tree visualisation, Variant calling Genomics, Model organisms, DNA polymorphism, Phylogenetics Genomics, Model organisms, DNA polymorphism, Phylogenetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snippy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snippy snippy snippy Rapid haploid variant calling and core SNP phylogeny generation. 3 3483 3838 188403 199916 4057 4306 138187 142349 2223 2852 67168 78979 60 60 8769 8769 430013 402527 11056 9823 +snp_dists snp_dists tabular Compute pairwise SNP distance matrix from a FASTA sequence alignment 2019-10-18 https://github.com/tseemann/snp-dists @TOOL_VERSION@ snp-dists 1.2.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-dists /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snp-dists 1 1166 1178 9794 10000 353 353 8021 8021 282 282 2937 2937 0 0 0 0 20958 20752 1813 1801 +snp_sites snp_sites fasta, vcf, phylip, tabular Finds SNP sites from a multi-FASTA alignment file 2017-06-28 https://github.com/sanger-pathogens/snp-sites @TOOL_VERSION@ snp-sites 2.5.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snp-sites /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snp-sites 1 990 1009 10043 10330 466 466 3029 3029 166 168 3008 3022 0 0 0 0 16381 16080 1643 1622 +snpeff snpEff, snpEff_build_gb, snpEff_databases, snpEff_download, snpEff_get_chr_names vcf, html, tabular, txt, snpeffdb, fasta SnpEff is a genetic variant annotation and effect prediction toolbox 2014-11-11 http://snpeff.sourceforge.net/ 5.4 biopython 1.70 To update Genome-Wide Association Study, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpeff /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/snpeff 5 5886 6736 100316 146690 9237 14794 119649 216751 1196 1451 15667 18565 401 403 1954 4043 386049 237586 23384 16720 +snpeff_sars_cov_2 snpeff_sars_cov_2 vcf, html, csv SnpEff, the COVID-19 version, is a genetic variant annotation and effect prediction toolbox 2020-06-17 http://snpeff.sourceforge.net/ @WRAPPER_VERSION@ To update Genome-Wide Association Study, Variant Analysis SNP detection SNP detection DNA polymorphism, Genetic variation, Nucleic acid sites, features and motifs DNA polymorphism, Nucleic acid sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpeff-covid19 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snpeff-covid19 snpeff snpEff Variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes and proteins (such as amino acid changes). 1 1580 1592 704888 766978 1876 1910 84580 99497 607 607 30784 32363 29 29 3465 3465 902303 823717 4138 4092 +snpfreqplot snpfreqplot pdf A plotting app to visualise the SNPs across a region 2020-12-02 https://github.com/BrownfieldPlantLab/SNPFreqPlot @VERSION@+galaxy@GALAXY_VERSION@ r-base To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/snpfreqplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/snpfreqplot 1 399 399 3862 3862 525 525 1655 1655 103 103 1386 1386 9 9 347 347 7250 7250 1036 1036 +snpsift snpSift_annotate, snpSift_caseControl, snpSift_extractFields, snpSift_filter, snpSift_int, snpSift_rmInfo, snpsift_vartype, snpSift_vcfCheck vcf, tabular, txt snpEff SnpSift tools from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html 5.4.0c snpsift 5.4.0c Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/snpsift/snpsift microbiome/pathogen-detection-from-nanopore-foodborne-data 8 2060 2117 5092180 5175645 3160 4102 368540 447226 502 515 105403 108005 39 40 11506 11523 5742399 5577629 6774 5761 +snpsift_dbnsfp snpSift_dbnsfp vcf snpEff SnpSift dbnsfp tool from Pablo Cingolani 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#dbNSFP 5.4.0c snpsift 5.4.0c Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_dbnsfp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/snpsift/snpsift_dbnsfp 1 21 25 70 82 62 77 297 425 0 0 0 0 0 0 0 0 507 367 102 83 +snpsift_genesets snpSift_geneSets vcf, txt Annotate SnpEff vcf with genesets such as Gene Ontology (GO), KEGG, Reactome 2014-11-11 http://snpeff.sourceforge.net/SnpSift.html#geneSets 5.4.0c snpsift 5.4.0c Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/snpsift/snpsift_genesets /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/snpsift/snpsift_genesets 1 105 149 570 644 179 218 437 534 0 0 0 0 0 0 0 0 1178 1007 367 284 +socru socru tabular, fasta, pdf Order and orientation of complete bacterial genomes 2019-09-03 https://github.com/quadram-institute-bioscience/socru 2.1.7 socru 2.2.5 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/socru /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/socru 1 41 52 571 679 90 107 278 320 0 0 0 0 0 0 0 0 999 849 159 131 +sonneityping sonneityping tabular Scripts for parsing Mykrobe predict results for Shigella sonnei. 2021-09-16 https://github.com/katholt/sonneityping 20210201 sonneityping 20210201 Up-to-date Sequence Analysis Antimicrobial resistance prediction, Variant calling, Genotyping Antimicrobial resistance prediction, Variant calling, Genotyping Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics Whole genome sequencing, Genotype and phenotype, Genetic variation, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sonneityping /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sonneityping sonneityping sonneityping Scripts for parsing Mykrobe predict results for Shigella sonnei. 1 2 2 2 2 0 0 0 0 0 0 0 0 0 0 0 0 2 2 2 2 +spacexr spacexr_cside, spacexr_rctd rds, txt, tabular Cell type identification and cell type-specific differential expression in spatial transcriptomics 2024-08-02 https://github.com/dmcable/spacexr/tree/master 2.2.1 r-spacexr 2.2.1 Up-to-date Spatial Omics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spacexr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spacexr 2 2 2 7 7 0 0 0 0 0 0 0 0 0 0 0 0 7 7 2 2 +spades spades_biosyntheticspades, spades_coronaspades, spades_metaplasmidspades, metaspades, spades_metaviralspades, spades_plasmidspades, rnaspades, spades_rnaviralspades, spades fasta, txt SPAdes is an assembly toolkit containing various assembly pipelines. It implements the following 4 stages: assembly graph construction, k-bimer adjustment, construction of paired assembly graph and contig construction. 2016-12-21 https://github.com/ablab/spades 4.3.0 spades 4.3.0 Up-to-date Assembly, RNA, Metagenomics Genome assembly Genome assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spades /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spades spades SPAdes St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. SPAdes 3.9 works with Illumina or IonTorrent reads and is capable of providing hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Additional contigs can be provided and can be used as long reads. microbiome/metagenomics-assembly 9 8250 8882 104429 116176 14023 14731 147425 154112 5211 6722 62902 76811 373 380 2677 2762 349861 317433 30715 27857 +spaln list_spaln_tables, spaln tabular Spaln (space-efficient spliced alignment) maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence. 2019-01-11 https://github.com/ogotoh/spaln 2.4.9 python To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spaln /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spaln 2 110 132 399 612 267 318 4249 4506 0 0 0 0 0 0 0 0 5118 4648 450 377 +spapros spapros_evaluation, spapros_selection png, pdf, svg, tabular Select and evaluate probe sets for targeted spatial transcriptomics. 2024-08-25 https://github.com/theislab/spapros 0.1.5 spapros 0.1.6 To update Single Cell, Transcriptomics, Sequence Analysis Primer and probe design, Visualisation Primer and probe design, Visualisation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spapros /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spapros spapros spapros Spapros is a python package that provides a pipeline for probe set selection and evaluation for targeted spatial transcriptomics data. 2 1 1 3 3 0 0 0 0 0 0 0 0 0 0 0 0 3 3 1 1 +spatialdata spatialdata_io, spatialdata_operation, spatialdata_plot spatialdata.zip, tabular, json, h5ad, jpg An open and universal framework for processing spatial omics data 2025-11-06 https://github.com/scverse/spatialdata 0.7.2 spatialdata To update Spatial Omics, Single Cell iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spatialdata /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spatialdata 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +spotyping spotyping txt, excel.xls, pdf SpoTyping allows fast and accurate in silico Mycobacterium spoligotyping from sequence reads 2018-05-08 https://github.com/xiaeryu/SpoTyping-v2.0 2.1 spotyping 2.1 Up-to-date Sequence Analysis Variant pattern analysis Variant pattern analysis Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation Microbiology, Sequencing, Sequence composition, complexity and repeats, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spotyping /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spotyping spotyping SpoTyping Fast and accurate in silico Mycobacterium spoligotyping from sequence reads. 1 34 34 2042 2042 0 0 0 0 0 0 0 0 0 0 0 0 2042 2042 34 34 +spyboat spyboat tiff, html Wavelet analysis for 3d-image stacks 2020-11-28 http://github.com/tensionhead/spyboat @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ spyboat To update Imaging, Graphics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/spyboat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/spyboat 1 6 6 174 174 0 0 0 0 0 0 0 0 0 0 0 0 174 174 6 6 +squidpy squidpy_graph, squidpy_plot spatialdata.zip, h5ad, png, pdf, svg, jpg Squidpy - Spatial Single Cell Analysis in Python 2026-02-27 https://squidpy.readthedocs.io 1.8.1 To update Single Cell, Spatial Omics, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squidpy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/squidpy 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +squirrel squirrel_phylo, squirrel_qc nexus, fasta, svg, png, csv QC and Phylogenetic analysis of MPXV 2025-01-16 https://github.com/aineniamh/squirrel 1.0.13 squirrel 1.3.2 To update Phylogenetics Phylogenetic analysis, Sequencing quality control Phylogenetic analysis, Sequencing quality control Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/squirrel /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/squirrel squirrel squirrel Some QUIck Reconstruction to Resolve Evolutionary LinksSquirrel provides a rapid way of producing reliable alignments for MPXV and also enable maximum-likelihood phylogenetics pipeline tree estimation. 2 2 2 7 7 0 0 0 0 41 41 193 193 0 0 0 0 200 200 43 43 +sra_tools fasterq_dump, fastq_dump, sam_dump txt NCBI Sequence Read Archive toolkit utilities 2015-11-17 https://github.com/ncbi/sra-tools 3.1.1 sra-tools 3.4.1 To update Data Source, Fastq Manipulation Data handling Data handling DNA, Genomics, Sequencing DNA, Genomics, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/sra-tools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/sra-tools sra-tools SRA Software Toolkit The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. https://usegalaxy.eu/published/workflow?id=08f41680101a1a45, https://workflowhub.eu/workflows/1103?version=3, https://workflowhub.eu/workflows/1104?version=2 3 12471 13217 237033 441031 27873 35613 529630 790405 3415 3922 56240 63877 411 416 6530 6602 1301915 829433 53168 44170 +srst2 srst2 tabular, fasta SRST2 Short Read Sequence Typing for Bacterial Pathogens 2022-08-22 http://katholt.github.io/srst2/ 0.2.0 samtools 1.23.1 To update Metagenomics Multilocus sequence typing Multilocus sequence typing Whole genome sequencing, Public health and epidemiology, Comparative genomics Whole genome sequencing, Public health and epidemiology, Comparative genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/srst2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/srst2 srst2 srst2 Short Read Sequence Typing for Bacterial Pathogens 1 68 68 407 407 1 1 71 71 0 0 0 0 0 0 0 0 478 478 69 69 +ssiamb ssiamb_self tabular ambiguous SNV counter from reads mapped back to their assembly. 2026-06-23 https://github.com/ssi-dk/ssiamb 1.0.0 ssiamb 1.0.0 Up-to-date Variant Analysis Genetic variation analysis Genetic variation analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ssiamb /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ssiamb ssiamb ssiamb ssiamb maps the reads back to the assembly, calls variants with BBTools, groups same-position VCF records, and counts ambiguous SNV loci using depth and minor allele frequency thresholds. 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +stacks stacks_assembleperead, stacks_clonefilter, stacks_cstacks, stacks_denovomap, stacks_genotypes, stacks_populations, stacks_procrad, stacks_pstacks, stacks_refmap, stacks_rxstacks, stacks_sstacks, stacks_stats, stacks_ustacks fasta, fastqsanger.gz, txt, html, tabular Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2016-03-07 http://catchenlab.life.illinois.edu/stacks/ @WRAPPER_VERSION@.1 stacks 2.68 To update Sequence Analysis Data handling Data handling Mapping, Population genetics Mapping, Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/stacks stacks Stacks Developed to work with restriction enzyme based sequence data, such as RADseq, for building genetic maps and conducting population genomics and phylogeography analysis. 13 132 199 6924 14189 0 0 0 0 40 40 6127 6127 2 2 8 8 20324 13059 241 174 +stacks2 stacks2_clonefilter, stacks2_cstacks, stacks2_denovomap, stacks2_gstacks, stacks2_kmerfilter, stacks2_populations, stacks2_procrad, stacks2_refmap, stacks2_shortreads, stacks2_sstacks, stacks2_tsv2bam, stacks2_ustacks tabular, txt Stacks is a software pipeline for building loci from short-read sequences, such as RAD-seq 2018-12-01 http://catchenlab.life.illinois.edu/stacks/ 2.55 stacks 2.68 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stacks2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/stacks2 12 118 145 8146 11221 0 0 0 0 54 54 22200 22427 8 9 650 651 34299 30996 208 180 +star_fusion star_fusion tabular STAR Fusion detects fusion genes in RNA-Seq data after running RNA-STAR 2015-10-15 https://github.com/STAR-Fusion/STAR-Fusion 0.5.4-3 star-fusion 1.15.1 To update Sequence Analysis, Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/star_fusion /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/star_fusion 1 84 108 1268 1483 204 337 1678 3284 4 4 300 300 0 0 0 0 5067 3246 449 292 +staramr staramr_search tabular, txt, xlsx Scan genome contigs against the ResFinder, PlasmidFinder, and PointFinder antimicrobial resistance databases. 2024-09-19 https://github.com/phac-nml/staramr @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ staramr 0.12.3 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction Microbiology, Public health and epidemiology, Infectious disease Microbiology, Public health and epidemiology, Infectious disease iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/staramr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/staramr staramr staramr staramr (*AMR) scans bacterial genome contigs against the ResFinder, PointFinder, and PlasmidFinder databases (used by the ResFinder webservice and other webservices offered by the Center for Genomic Epidemiology) and compiles a summary report of detected antimicrobial resistance genes. The star|* in staramr indicates that it can handle all of the ResFinder, PointFinder, and PlasmidFinder databases. microbiome/plasmid-metagenomics-nanopore 1 2921 3072 31443 33124 2130 2130 14763 14763 1173 1182 8989 9237 97 97 9838 9838 66962 65033 6481 6321 +straindesign straindesign_analyzing_model, straindesign_reduce_model, straindesign_simulate_deletion png, sbml, tabular Toolbox to optimize biological model 2022-10-02 https://github.com/brsynth/straindesign 3.2.2 straindesign 3.2.3 To update Systems Biology, Synthetic Biology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/straindesign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/straindesign 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +strelka strelka_germline, strelka_somatic vcf, bed Strelka2 is a fast and accurate small variant caller optimizedfor analysis of germline variation in small cohorts and somaticvariation in tumor/normal sample pairs. The germline caller employs anefficient tiered haplotype model to improve accuracy and provide read-backedphasing, adaptively selecting between assembly and a faster alignment-basedhaplotyping approach at each variant locus. The germline caller also analyzesinput sequencing data using a mixture-model indel error estimation method toimprove robustness to indel noise. The somatic calling model improves on theoriginal Strelka method for liquid and late-stage tumor analysis by accountingfor possible tumor cell contamination in the normal sample. A final empiricalvariant re-scoring step using random forest models trained on various callquality features has been added to both callers to further improve precision. 2021-01-27 https://github.com/Illumina/strelka/ 2.9.10 strelka 2.9.10 Up-to-date Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/strelka /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/strelka 2 88 88 992 992 342 342 1990 1990 0 0 0 0 0 0 0 0 2982 2982 430 430 +stringtie stringtie, stringtie_merge gtf, tabular StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. 2014-09-13 http://ccb.jhu.edu/software/stringtie/ 3.0.3 stringtie 3.0.3 Up-to-date Transcriptomics Transcriptome assembly, RNA-Seq analysis Transcriptome assembly, RNA-Seq analysis Transcriptomics, RNA-Seq Transcriptomics, RNA-Seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/stringtie /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/stringtie stringtie StringTie Fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. https://usegalaxy.eu/published/workflow?id=96c61a584cb2e5e9, https://usegalaxy.eu/published/workflow?id=aff44f1665a14e23, https://usegalaxy.eu/published/workflow?id=b426e137396acb14, https://usegalaxy.eu/published/workflow?id=deec04097a871646 2 3884 4419 194508 217287 6876 11163 316022 446115 673 865 27958 33201 302 303 3783 3787 700390 542271 16750 11735 +structure structure txt for using multi-locus genotype data to investigate population structure. 2017-09-22 https://web.stanford.edu/group/pritchardlab/structure.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ structure 2.3.4 To update Phylogenetics, Variant Analysis Genetic variation analysis Genetic variation analysis Population genetics Population genetics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structure /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/structure structure Structure The program structureis a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. 1 138 155 3903 4354 0 0 0 0 0 0 0 0 3 3 330 330 4684 4233 158 141 +structureharvester structureharvester txt for parsing STRUCTURE outputs and for performing the Evanno method 2017-12-06 http://alumni.soe.ucsc.edu/~dearl/software/structureHarvester/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ structureharvester 0.6.94 To update Phylogenetics, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/structureharvester /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/structureharvester 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +suite_pretext pretext_graph, pretext_map, pretext_snapshot pretext Process genome contacts maps processing images. 2021-04-05 https://github.com/wtsi-hpag/PretextSnapshot @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ pretextgraph 0.0.9 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/pretext /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/pretext 3 397 397 5173 5173 241 241 6703 6703 53 53 1729 1729 0 0 0 0 13605 13605 691 691 +swiftlink swiftlink allegro_fparam, txt Parallel MCMC Linkage Analysis 2017-11-21 https://github.com/ajm/swiftlink @VERSION@.0 swiftlink 1.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/swift /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/swift 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +swissmodel_modelling_api swissmodel_modelling_api Fully automated protein structure homology-modelling 2025-12-11 https://swissmodel.expasy.org @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ python To update Proteomics Protein modelling, Protein modelling (backbone) Protein modelling Molecular modelling, Proteins, Molecular interactions, pathways and networks, Protein structure analysis, Structure prediction Molecular modelling, Molecular interactions, pathways and networks, Protein structure analysis, Structure prediction iuc https://github.com/galaxyproject/tools-iuc/main/tools/swissmodel_modelling_api /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/swissmodel_modelling_api swiss_model SWISS-MODEL SWISS-MODEL is a fully automated protein structure homology-modelling server, accessible via the ExPASy web server, or from the program DeepView (Swiss Pdb-Viewer). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists worldwide. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +syndiva syndiva html SynDivA was developed to analyze the diversity of synthetic libraries of a Fibronectin domain. 2022-06-24 1.0 clustalo 1.2.4 To update Proteomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syndiva /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/syndiva 1 2 2 30 30 0 0 0 0 0 0 0 0 0 0 0 0 30 30 2 2 +syri syri tabular, vcf Synteny and Rearrangement Identifier 2025-04-16 https://github.com/schneebergerlab/syri 1.7.1 syri 1.7.1 Up-to-date Sequence Analysis Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping Haplotype mapping, Variant calling, Genotyping, Sequence assembly, Read mapping DNA polymorphism, Sequence assembly, DNA structural variation, Mapping, Sequencing DNA polymorphism, Sequence assembly, Mapping, Sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/syri /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/syri SyRI SyRI SyRI is tool for finding genomic rearrangements and local sequence differences from whole-genome assemblies.Genomic differences range from single nucleotide differences to complex structural variations. Current methods typically annotate sequence differences ranging from SNPs to large indels accurately but do not unravel the full complexity of structural rearrangements, including inversions, translocations, and duplications, where highly similar sequence changes in location, orientation, or copy number. Here, we present SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions. 1 22 22 84 84 0 0 0 0 0 0 0 0 5 5 76 76 160 160 27 27 +table_compute table_compute tabular Perform general-purpose table operations 2019-06-05 https://github.com/galaxyproject/tools-iuc/tree/master/tools/table_compute @VERSION@+galaxy@WRAPPER_VERSION@ pandas To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/table_compute /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/table_compute microbiome/pathogen-detection-from-nanopore-foodborne-data 1 1946 2210 235082 237980 1655 1819 12248 14832 262 285 17101 18230 99 100 892 926 271968 265323 4414 3962 +tabular_to_fastq tabular_to_fastq fastq Tabular to FASTQ converter 2019-06-21 https://github.com/galaxyproject/sequence_utils 1.2 galaxy_sequence_utils 1.2.0 To update Fastq Manipulation devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/galaxy_sequence_utils/tabular_to_fastq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/galaxy_sequence_utils/tabular_to_fastq 1 507 586 9277 11798 740 2407 7442 32030 92 124 892 1250 11 12 20 22 45100 17631 3129 1350 +taffy taffy_add_gap_bases, taffy_annotate, taffy_coverage, taffy_norm, taffy_sort, taffy_stats, taffy_view taf, tabular A set of tools for manipulating TAF files 2026-03-24 https://github.com/ComparativeGenomicsToolkit/cactus 0.0.3 taffy 0.0.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taffy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/taffy 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +tag_pileup_frequency tag_pileup_frequency tabular Contains a tool that generates a frequency pileup of the 5' ends of aligned reads in a BAM filerelative to reference points in a BED file. 2016-05-05 https://github.com/seqcode/cegr-tools/tree/master/src/org/seqcode/cegrtools/tagpileup 1.0.2 openjdk To update Statistics, SAM, Genomic Interval Operations iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tag_pileup_frequency /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tag_pileup_frequency 1 11 17 35 184 34 77 661 875 0 0 0 0 0 0 0 0 1059 696 94 45 +tasmanian_mismatch tasmanian_mismatch txt, html Analysis of positional mismatches 2020-04-19 https://github.com/nebiolabs/tasmanian-mismatch @TOOL_VERSION@ tasmanian-mismatch 2.0.2 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tasmanian_mismatch /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tasmanian_mismatch 1 11 11 23 23 32 32 292 292 0 0 0 0 0 0 0 0 315 315 43 43 +taxonkit name2taxid, profile2cami tabular, tsv TaxonKit - A Practical and Efficient NCBI Taxonomy Toolkit 2024-07-26 https://bioinf.shenwei.me/taxonkit/ 0.20.0 taxonkit 0.20.0 Up-to-date Metagenomics Formatting, Data retrieval Formatting, Data retrieval Taxonomy, Biotechnology, Ecology Taxonomy, Biotechnology, Ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/taxonkit taxonkit TaxonKit TaxonKit is a practical and efficient NCBI taxonomy toolkit. 2 12 12 1094 1094 0 0 0 0 0 0 0 0 0 0 0 0 1094 1094 12 12 +taxonomy_filter_refseq taxonomy_filter_refseq fasta Filter RefSeq by taxonomy 2019-01-13 https://github.com/pvanheus/ncbitaxonomy @TOOL_VERSION@ rust-ncbitaxonomy 1.1.0 To update Sequence Analysis, Genome annotation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_filter_refseq /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/taxonomy_filter_refseq 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +taxonomy_krona_chart taxonomy_krona_chart html Krona pie chart from taxonomic profile 2015-08-06 http://sourceforge.net/projects/krona/ 2.7.1 krona 2.8.1 To update Assembly Visualisation Visualisation Metagenomics Metagenomics crs4 https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxonomy_krona_chart /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/taxonomy_krona_chart krona Krona Krona creates interactive HTML5 charts of hierarchical data (such as taxonomic abundance in a metagenome). https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b14845359b702444, https://usegalaxy.eu/published/workflow?id=d05c6f0f3205fbd2 microbiome/beer-data-analysis, microbiome/general-tutorial, microbiome/metatranscriptomics, microbiome/metatranscriptomics-short, microbiome/mothur-miseq-sop, microbiome/nanopore-16S-metagenomics, microbiome/pathogen-detection-from-nanopore-foodborne-data, microbiome/taxonomic-profiling 1 7406 7874 48617 51653 6438 7659 33268 41191 2005 2042 11003 11192 162 163 565 586 104622 93453 17738 16011 +taxpasta taxpasta tabular, biom1 standardise taxonomic profiles 2023-08-30 https://taxpasta.readthedocs.io/en/latest/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ taxpasta 0.7.0 To update Sequence Analysis Standardisation and normalisation, Aggregation, Formatting, Conversion Standardisation and normalisation, Aggregation, Formatting, Conversion Taxonomy, Metagenomics Taxonomy, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/taxpasta /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/taxpasta taxpasta taxpasta TAXonomic Profile Aggregation and STAndardisationThe main purpose of taxpasta is to standardise taxonomic profiles created by a range of bioinformatics tools. We call those tools taxonomic profilers. They each come with their own particular tabular output format. Across the profilers, relative abundances can be reported in read counts, fractions, or percentages, as well as any number of additional columns with extra information. We therefore decided to take the lessons learnt to heart and provide our own solution to deal with this pasticcio. With taxpasta you can ingest all of those formats and, at a minimum, output taxonomy identifiers and their integer counts. Taxpasta can not only standardise profiles but also merge them across samples for the same profiler into a single table. https://usegalaxy.eu/published/workflow?id=b14845359b702444 1 51 51 323 323 0 0 0 0 0 0 0 0 1 1 18 18 341 341 52 52 +tb-profiler tb_profiler_collate, tb_profiler_profile tabular, csv, txt, json, vcf, bam, pdf Processes M. tuberculosis sequence data to infer strain type and identify known drug resistance markers. 2019-04-02 https://github.com/jodyphelan/TBProfiler 6.6.5 tb-profiler 6.7.0 To update Sequence Analysis Antimicrobial resistance prediction Antimicrobial resistance prediction iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb-profiler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tb-profiler tb-profiler tb-profiler A tool for drug resistance prediction from _M. tuberculosis_ genomic data (sequencing reads, alignments or variants). 2 491 535 15947 16201 490 506 11483 11641 199 201 10939 10981 0 0 0 0 38823 38369 1242 1180 +tb_variant_filter tb_variant_filter vcf M. tuberculosis H37Rv VCF filter 2019-10-03 https://github.com/COMBAT-TB/tb_variant_filter @TOOL_VERSION@ tb_variant_filter 0.4.0 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tb_variant_filter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tb_variant_filter 1 618 655 43892 44301 356 364 23229 23483 103 103 10184 10203 1 1 3000 3000 80987 80305 1123 1078 +tbl2gff3 tbl2gff3 gff3 Table to GFF3 2020-07-07 https://github.com/galaxyproject/tools-iuc/tree/master/tools/tbl2gff3 1.2 bcbiogff 0.6.6 To update Convert Formats, Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbl2gff3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tbl2gff3 1 661 661 2492 2492 255 255 604 604 148 148 649 649 17 17 53 53 3798 3798 1081 1081 +tbvcfreport tbvcfreport html, txt Generate HTML report from SnpEff M.tuberculosis VCF(s) 2019-08-29 https://github.com/COMBAT-TB/tbvcfreport @TOOL_VERSION@ tbvcfreport 1.0.1 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tbvcfreport /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tbvcfreport 1 378 411 9773 9913 418 441 7332 7415 96 97 3675 3682 1 1 1 1 21011 20781 950 893 +te_finder te_finder bed, gtf, bam Transposable element insertions finder 2022-08-09 https://github.com/VistaSohrab/TEfinder 1.0.1 samtools 1.23.1 To update Sequence Analysis Genome indexing, Variant calling, PCR primer design Genome indexing, Variant calling, PCR primer design Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation Sequencing, Mobile genetic elements, Workflows, Evolutionary biology, Genetic variation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/te_finder /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/te_finder tefinder TEfinder A Bioinformatics Pipeline for Detecting New Transposable Element Insertion Events in Next-Generation Sequencing Data.A bioinformatics tool for detecting novel transposable element insertions.TEfinder uses discordant reads to detect novel transposable element insertion events in paired-end sample sequencing data. 1 28 28 219 219 0 0 0 0 0 0 0 0 0 0 0 0 219 219 28 28 +telescope_assign telescope_assign tabular, bam Single locus resolution of Transposable ELEment expression. 2019-09-03 https://github.com/mlbendall/telescope/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ telescope 1.0.4 To update Genome annotation Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping Essential dynamics, Sequence trimming, RNA-Seq quantification, Expression analysis, Read mapping RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly RNA-Seq, Transcriptomics, Mapping, Gene transcripts, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/telescope /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/telescope Telescope-expression Telescope Telescope is a tool for the characterization of the retrotranscriptome by accurate estimation of transposable element expression and the quantification of transposable element expression using RNA-seq.It can be used for Statistical Performance of TE Quantification Methods.All scripts needed to examine the sensitivity and biases of computational approaches for quantifying TE expression: 1) unique counts, 2) best counts, 3) RepEnrich, 4) TEtranscripts, 5) RSEM, 6) SalmonTE, and 7) Telescope. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +telogator telogator, telogator_make_ref tabular, png, fasta Measure allele-specific telomere length from long-read sequencing data 2025-12-04 https://github.com/zstephens/telogator2 2.2.3 telogator2 2.2.3 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/telogator /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/telogator telogator2 telogator2 A method for measuring allele-specific TL and characterizing telomere variant repeat (TVR) sequences from long reads. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +teloscope teloscope bed, tabular, bedgraph Teloscope is a fast and comprehensive tool for matching, counting, and reporting telomeric repeats from genome assemblies. 2025-11-27 https://github.com/vgl-hub/teloscope 0.1.3 teloscope 0.1.3 Up-to-date Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/teloscope /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/teloscope 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +tesseract tesseract txt, pdf, html, tsv, xml Tesseract is an OCR engine with support for unicode and the ability to recognize more than 100 languages out of the box. 2025-06-18 https://github.com/tesseract-ocr/tesseract 5.5.2 tesseract 3.04.01 To update Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tesseract /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tesseract 1 10 10 83 83 0 0 0 0 0 0 0 0 0 0 0 0 83 83 10 10 +tetoolkit tetoolkit_tetranscripts tabular, txt The TEToolkit suite improves the bioinformatic analysis of repetitive sequences, particularly transposable elements, in order to elucidate novel (and previously ignored) biological insights of their functions in development and diseases. 2020-04-10 https://github.com/mhammell-laboratory/TEtranscripts @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ tetranscripts 2.2.4 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetoolkit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tetoolkit 1 89 93 1167 1200 0 0 0 0 5 5 206 206 0 0 0 0 1406 1373 98 94 +tetyper tetyper tabular, vcf, bam, txt Type a specific transposable element (TE) of interest from paired-end sequencing data. 2019-11-22 https://github.com/aesheppard/TETyper @TOOL_VERSION@ tetyper 1.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tetyper /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tetyper 1 23 25 146 178 50 57 142 200 0 0 0 0 0 0 0 0 378 288 82 73 +tiberius tiberius gtf Tiberius is a tool for deep learning-based ab initio gene structure prediction 2026-04-23 https://github.com/Gaius-Augustus/Tiberius 2.0.5 To update Genome annotation Genome annotation Genome annotation Genomics Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tiberius /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tiberius tiberius Tiberius End-to-End Deep Learning with an HMM for Gene Prediction 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +tn93 tn93_readreduce, tn93, tn93_cluster, tn93_filter fasta, csv, json Compute distances between sequences 2018-06-06 https://github.com/veg/tn93/ 1.0.16 tn93 1.0.16 Up-to-date Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tn93 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tn93 4 31 31 1952 1952 86 102 2566 2831 0 0 0 0 0 0 0 0 4783 4518 133 117 +tooldistillator tooldistillator, tooldistillator_summarize txt, json ToolDistillator extract and aggregate information from different tool outputs to JSON parsable files 2024-04-30 https://gitlab.com/ifb-elixirfr/abromics/tooldistillator 1.0.6 tooldistillator 1.0.6 Up-to-date Sequence Analysis Data parsing Microbiology, Bioinformatics, Sequence analysis Microbiology, Bioinformatics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tooldistillator /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tooldistillator tooldistillator ToolDistillator ToolDistillator is a tool to extract information from output files of specific tools, expose it as JSON files, and aggregate over several tools.It can produce both a single file to each tool or a summarized file from a set of reports. https://usegalaxy.eu/published/workflow?id=2fa2f67603772413, https://usegalaxy.eu/published/workflow?id=7e48134082dab0a3 2 121 121 5042 5042 162 162 1550 1550 0 0 0 0 9 9 19253 19253 25845 25845 292 292 +tracegroomer tracegroomer tabular TraceGroomer is a solution for formatting and normalising Tracer metabolomics given file(s), to produce the .csv files which are ready for DIMet tool. 2024-03-28 https://github.com/cbib/TraceGroomer 0.1.4 tracegroomer 0.1.4 Up-to-date Metabolomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracegroomer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tracegroomer 1 2 2 16 16 0 0 0 0 0 0 0 0 4 4 42 42 58 58 6 6 +tracy tracy_align, tracy_assemble, tracy_basecall, tracy_decompose txt, fasta, json, bcf A suite tools for basecalling, alignment, assembly and deconvolution of Sanger chromatograms using tracy. 2021-10-12 https://github.com/gear-genomics/tracy/ 0.7.8 tracy 0.8.1 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tracy /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tracy 4 55 55 4837 4837 0 0 0 0 0 0 0 0 0 0 0 0 4837 4837 55 55 +transdecoder transdecoder fasta, gff3, bed, zip, txt TransDecoder finds coding regions within transcripts 2015-11-09 https://transdecoder.github.io/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ transdecoder 6.0.0 To update Transcriptomics, RNA Coding region prediction, de Novo sequencing, De-novo assembly Coding region prediction, de Novo sequencing, De-novo assembly Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing Genomics, Gene transcripts, RNA-Seq, Gene expression, Sequence assembly, Whole genome sequencing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transdecoder /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/transdecoder TransDecoder TransDecoder TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. 1 1215 1323 7178 8593 1267 1357 6450 7010 372 432 3197 3705 37 38 495 505 19813 17320 3150 2891 +transit gff_to_prot, transit_gumbel, transit_hmm, transit_resampling, transit_tn5gaps tabular TRANSIT 2019-03-01 https://github.com/mad-lab/transit/ 3.2.3 transit 3.3.20 To update Genome annotation Transposon prediction Transposon prediction DNA, Sequencing, Mobile genetic elements DNA, Sequencing, Mobile genetic elements iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/transit transit TRANSIT A tool for the analysis of Tn-Seq data. It provides an easy to use graphical interface and access to three different analysis methods that allow the user to determine essentiality in a single condition as well as between conditions. 5 97 104 1908 2076 210 244 2813 4134 42 42 640 640 0 0 0 0 6850 5361 390 349 +transtermhp transtermhp gff3 Finds rho-independent transcription terminators in bacterial genomes 2015-10-08 https://transterm.cbcb.umd.edu @WRAPPER_VERSION@.1 transtermhp 2.09 To update Sequence Analysis Transcriptional regulatory element prediction Transcriptional regulatory element prediction Transcription factors and regulatory sites Transcription factors and regulatory sites iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/transtermhp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/transtermhp transtermhp TransTermHP TransTermHP finds rho-independent transcription terminators in bacterial genomes. Each terminator found by the program is assigned a confidence value that estimates its probability of being a true terminator 1 59 62 467 502 49 55 170 216 0 0 0 0 0 0 0 0 718 637 117 108 +trimal trimal html, txt Tool for automated alignment trimming 2024-10-02 https://trimal.readthedocs.io @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ trimal 1.5.1 To update Sequence Analysis, Phylogenetics Multiple sequence alignment Multiple sequence alignment Sequence analysis, Sequencing, Sequence sites, features and motifs Sequence analysis, Sequencing, Sequence sites, features and motifs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimal /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/trimal trimal trimAl Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment. 1 173 173 2180 2180 0 0 0 0 4 4 32 32 115 115 1230 1230 3442 3442 292 292 +trimmomatic trimmomatic txt A flexible read trimming tool for Illumina NGS data 2024-01-03 http://www.usadellab.org/cms/?page=trimmomatic 0.39 trimmomatic 0.40 To update Fastq Manipulation pjbriggs https://github.com/galaxyproject/tools-iuc/tree/main/tools/trimmomatic /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/trimmomatic https://usegalaxy.eu/published/workflow?id=1ef76b7b86e15792, https://usegalaxy.eu/published/workflow?id=466bdd8ba7b67264, https://usegalaxy.eu/published/workflow?id=b7166aff73e5d81c 1 18851 20991 437833 502595 45190 60956 714562 1020864 6132 7428 144168 173860 1010 1011 37524 37543 1734862 1334087 90386 71183 +trimns trimns fasta TrimNs is used to trim and remove fake cut sites from bionano hybrid scaffold data in the VGP pipeline 2021-01-29 https://github.com/VGP/vgp-assembly/tree/master/pipeline/bionano/trimNs 0.1.0 trimns_vgp 1.0 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/TrimNs /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/TrimNs 1 25 25 49 49 0 0 0 0 0 0 0 0 0 0 0 0 49 49 25 25 +trinity trinity_abundance_estimates_to_matrix, trinity_align_and_estimate_abundance, trinity_analyze_diff_expr, trinity_contig_exn50_statistic, trinity_define_clusters_by_cutting_tree, describe_samples, trinity_filter_low_expr_transcripts, trinity_gene_to_trans_map, trinity_run_de_analysis, trinity_samples_qccheck, trinity_super_transcripts, trinity, trinity_stats tabular, rdata, pdf, fasta, gtf, clustal, txt Trinity represents a method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq datahttps://github.com/trinityrnaseq/trinityrnaseq 2015-11-09 https://github.com/trinityrnaseq/trinityrnaseq 2.15.1 trinity 2.15.2 To update Transcriptomics, RNA Transcriptome assembly Transcriptome assembly Transcriptomics, Gene expression, Gene transcripts Transcriptomics, Gene transcripts iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinity /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/trinity trinity Trinity Trinity is a transcriptome assembler which relies on three different tools, inchworm an assembler, chrysalis which pools contigs and butterfly which amongst others compacts a graph resulting from butterfly with reads. 13 2033 2319 42409 52163 3769 4091 48710 53240 809 933 22208 30291 155 159 3279 3411 139105 116606 7502 6766 +trinotate trinotate tabular, sqlite Trinotate is a comprehensive annotation suite designed for automatic functional annotation of de novo transcriptomes. 2016-11-15 https://trinotate.github.io/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ trinotate 4.0.2 To update Transcriptomics, RNA Gene functional annotation Gene functional annotation Gene expression, Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trinotate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/trinotate trinotate Trinotate Comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. 1 458 517 2157 2558 549 598 2012 2211 170 224 950 1284 0 1 0 10 6063 5119 1340 1177 +trycycler trycycler_cluster, trycycler_consensus, trycycler_partition, trycycler_reconcile_msa, trycycler_subsample phylip, newick, fasta Trycycler toolkit wrappers 2021-02-11 https://github.com/rrwick/Trycycler 0.5.5 trycycler 0.5.6 To update Assembly Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Genome assembly, Sequence trimming, Scaffold gap completion, Sequence assembly validation Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics Sequence assembly, DNA, Human biology, Whole genome sequencing, Genomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/trycycler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/trycycler trycycler Trycycler Trycycler: consensus long-read assemblies for bacterial genomes 5 122 122 15743 15743 0 0 0 0 57 57 6233 6233 3 3 27 27 22003 22003 182 182 +tsebra tsebra gtf, txt This tool has been developed to combine BRAKER predictions. 2023-10-19 https://github.com/Gaius-Augustus/TSEBRA 1.1.2.5 tsebra 1.1.2.5 Up-to-date Genome annotation Homology-based gene prediction, Alternative splicing prediction Homology-based gene prediction, Alternative splicing prediction Gene expression, RNA-Seq, Gene transcripts, Model organisms Gene expression, RNA-Seq, Gene transcripts, Model organisms iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsebra /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tsebra tsebra TSEBRA TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER1 and BRAKER2 predicitons to increase their accuracies. 1 16 16 51 51 0 0 0 0 0 0 0 0 0 0 0 0 51 51 16 16 +tsenat tsenat tabular, txt, png TSENAT - Tsallis entropy analysis for transcript-level isoform complexity 2026-06-01 https://github.com/gallardoalba/TSENAT 0.99.0 r-tsenat 0.99.0 Up-to-date Transcriptomics, RNA, Statistics RNA-Seq analysis RNA-Seq analysis Transcriptomics Transcriptomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsenat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tsenat tsenat TSENAT TSENAT is a R package for quantifying and modeling isoform-usage complexity across RNA-seq samples using Tsallis entropy, a scale-dependent information-theoretic measure of transcript heterogeneity. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +tsne tsne pdf T-Distributed Stochastic Neighbor Embedding using a Barnes-Hut Implementation 2017-05-26 https://cran.r-project.org/web/packages/Rtsne/ 0.0.2 r-rtsne 0.13 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tsne /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tsne 1 25 39 163 382 60 69 275 305 0 0 0 0 2 2 4 4 691 442 110 87 +tximport tximport tabular Wrapper for the Bioconductor package tximport 2019-10-15 http://bioconductor.org/packages/tximport/ @TOOL_VERSION@ bioconductor-tximport 1.38.2 To update Transcriptomics Pathway or network analysis, Formatting, RNA-Seq analysis Pathway or network analysis, Formatting, RNA-Seq analysis Transcriptomics, Gene transcripts, Workflows Transcriptomics, Gene transcripts, Workflows iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/tximport /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/tximport tximport tximport An R/Bioconductor package that imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. 1 297 314 2388 2576 994 1081 7694 8341 0 0 0 0 0 0 0 0 10917 10082 1395 1291 +ucsc_axtchain ucsc_axtchain chain, txt Chain together genome alignments 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ucsc-axtchain 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axtchain /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_axtchain UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 57 57 0 0 0 0 0 0 0 0 57 57 4 4 +ucsc_axttomaf ucsc_axtomaf maf Convert dataset from axt to MAF format. 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-axttomaf 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_axttomaf /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_axttomaf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 59 59 0 0 0 0 0 0 0 0 59 59 4 4 +ucsc_blat ucsc_blat tabular Standalone blat sequence search command line tool 2017-05-17 http://genome.ucsc.edu/goldenPath/help/blatSpec.html @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ ucsc-blat 482 To update Sequence Analysis Sequence alignment Sequence alignment Sequence analysis Sequence analysis yating-l https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_blat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_blat blat BLAT Fast, accurate spliced alignment of DNA sequences. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ucsc_chainantirepeat ucsc_chainantirepeat chain Remove repeated chains 2025-03-07 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-chainantirepeat 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainantirepeat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_chainantirepeat UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 3 3 42 42 0 0 0 0 0 0 0 0 42 42 3 3 +ucsc_chainnet ucsc_chainnet ucsc.net Make alignment nets out of chains 2024-08-30 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-chainnet 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainnet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_chainnet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 61 61 0 0 0 0 0 0 0 0 61 61 4 4 +ucsc_chainprenet ucsc_chainprenet chain Remove chains that don't have a chance of being netted 2024-08-27 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-chainprenet 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainprenet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_chainprenet UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 60 60 0 0 0 0 0 0 0 0 60 60 4 4 +ucsc_chainsort ucsc_chainsort chain Sort chains. By default sorts by score. 2024-08-26 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-chainsort 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainsort /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_chainsort UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 60 60 0 0 0 0 0 0 0 0 60 60 4 4 +ucsc_chainswap ucsc_chainswap chain Swap target and query in a chain. 2026-01-25 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-chainswap 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_chainswap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_chainswap UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ucsc_fasplit fasplit faSplit is a tool to split a single FASTA file into several files 2017-09-08 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-fasplit 482 To update Fasta Manipulation Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fasplit /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/fasplit UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 554 602 3994 4315 689 777 6770 7638 212 218 1497 1540 8 8 38 38 13531 12299 1605 1463 +ucsc_fatovcf fatovcf vcf Convert a FASTA alignment file to Variant Call Format (VCF) single-nucleotide diffs 2023-01-11 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-fatovcf 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/fatovcf /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/fatovcf UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 72 72 515 515 205 205 1868 1868 13 13 226 226 0 0 0 0 2609 2609 290 290 +ucsc_maftoaxt maftoaxt axt Convert dataset from MAF to axt format 2024-07-30 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-maftoaxt 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/maftoaxt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/maftoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 3 3 11 11 0 0 0 0 0 0 0 0 11 11 3 3 +ucsc_netchainsubset ucsc_netchainsubset chain Create chain file with subset of chains that appear in the net 2026-01-14 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-netchainsubset 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netchainsubset /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_netchainsubset UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +ucsc_netfilter ucsc_netfilter ucsc.net Filter out parts of net 2024-09-18 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-netfilter 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netfilter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_netfilter UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 56 56 0 0 0 0 0 0 0 0 56 56 4 4 +ucsc_netsyntenic ucsc_netsyntenic ucsc.net Add synteny info to a net dataset 2024-09-04 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-netsyntenic 482 To update Sequence Analysis Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_netsyntenic /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_netsyntenic UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 6 6 72 72 0 0 0 0 0 0 0 0 72 72 6 6 +ucsc_nettoaxt ucsc_nettoaxt axt Convert net (and chain) to axt format. 2024-09-19 http://hgdownload.cse.ucsc.edu/admin/exe/ @TOOL_VERSION@ ucsc-nettoaxt 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/ucsc_nettoaxt /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/ucsc_nettoaxt UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 0 0 0 0 4 4 55 55 0 0 0 0 0 0 0 0 55 55 4 4 +ucsc_twobittofa ucsc-twobittofa fasta twoBitToFa is a tool to convert all or part of .2bit file to FASTA 2016-08-19 https://genome.ucsc.edu/goldenpath/help/twoBit.html @TOOL_VERSION@ ucsc-twobittofa 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/twobittofa /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/twobittofa UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 85 126 430 570 131 159 803 861 3 3 73 73 0 0 0 0 1504 1306 288 219 +ucsc_wigtobigwig ucsc_wigtobigwig bigwig converts bedGraph (wig) files into binary bigwig 2024-01-14 https://genome.ucsc.edu/goldenPath/help/bigWig.html @TOOL_VERSION@ ucsc-wigtobigwig 482 To update Convert Formats Sequence analysis Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/ucsc_tools/wigtobigwig /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/ucsc_tools/wigtobigwig UCSC_Genome_Browser_Utilities UCSC Genome Browser Utilities Utilities for handling sequences and assemblies from the UCSC Genome Browser project. 1 345 345 4562 4562 759 759 9257 9257 58 58 1088 1088 0 0 0 0 14907 14907 1162 1162 +umi-tools umi_tools_count, umi_tools_dedup, umi_tools_extract, umi_tools_group, umi_tools_whitelist tabular, bam, html UMI-tools extract - Extract UMIs from fastq 2017-08-09 https://github.com/CGATOxford/UMI-tools 1.1.6 umi_tools 1.1.6 Up-to-date Sequence Analysis, Transcriptomics, Single Cell Sequencing quality control Sequencing quality control NGS, Sequence sites, features and motifs, Quality affairs Sequence sites, features and motifs, Quality affairs iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/umi_tools /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/umi_tools umi-tools UMI-tools Tools for handling Unique Molecular Identifiers in NGS data sets. https://usegalaxy.eu/published/workflow?id=ca9d3233b0912765 5 568 710 48490 74207 637 637 12544 12796 109 118 17752 18006 5 5 48 48 105057 78834 1470 1319 +unicycler unicycler gfa1, fasta, bam Unicycler is a hybrid assembly pipeline for bacterial genomes. 2017-05-08 https://github.com/rrwick/Unicycler @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ unicycler 0.5.1 To update Assembly Genome assembly, Aggregation Genome assembly, Aggregation Microbiology, Genomics, Sequencing, Sequence assembly Microbiology, Genomics, Sequencing, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/unicycler /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/unicycler unicycler Unicycler A tool for assembling bacterial genomes from a combination of short (2nd generation) and long (3rd generation) sequencing reads. microbiome/plasmid-metagenomics-nanopore 1 4697 5202 83521 96874 5770 8769 65067 104850 2392 2613 22717 26831 272 276 2160 2183 230738 173465 16860 13131 +upsetplot rcx_upsetplot png, txt Upset plot visualization tool using UpSetR 2025-04-17 https://github.com/galaxyproject/tools-iuc @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ r-upsetr 1.0.3 To update Visualization iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/upsetr /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/upsetr 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +usher usher_matutils, usher_ripples, usher txt, tabular, vcf, protobuf3, json, newick UShER toolkit wrappers 2021-05-11 https://github.com/yatisht/usher 0.6.6 usher 0.6.6 Up-to-date Phylogenetics Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Classification, Phylogenetic tree visualisation, Phylogenetic inference (from molecular sequences) Phylogeny, Evolutionary biology, Cladistics, Genotype and phenotype, Phylogenomics Cladistics, Genotype and phenotype, Phylogenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/usher /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/usher usher usher The UShER toolkit includes a set of tools for for rapid, accurate placement of samples to existing phylogenies. While not restricted to SARS-CoV-2 phylogenetic analyses, it has enabled real-time phylogenetic analyses and genomic contact tracing in that its placement is orders of magnitude faster and more memory-efficient than previous methods. 3 5 5 1060 1060 0 0 0 0 0 0 0 0 0 0 0 0 1060 1060 5 5 +vader_sentiment vader_sentiment tabular VADER sentiment analysis for text 2026-05-20 https://github.com/cjhutto/vaderSentiment @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vadersentiment To update Text Manipulation, Natural Language Processing iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vader /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vader 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +valet valet pdf A pipeline for detecting mis-assemblies in metagenomic assemblies. 2017-11-16 https://github.com/marbl/VALET @WRAPPER_VERSION@.0 valet 1.0 To update Metagenomics Sequence assembly, Sequence assembly visualisation Sequence assembly, Sequence assembly visualisation Metagenomics, Sequence assembly Metagenomics, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/valet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/valet valet VALET VALET is a pipeline for detecting mis-assemblies in metagenomic assemblies. 1 74 101 449 711 67 76 160 249 0 0 0 0 0 0 0 0 960 609 177 141 +vapor vapor tabular, fasta Classify Influenza samples from raw short read sequence data 2022-08-24 https://github.com/wm75/vaporup @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vapor 1.0.3 To update Sequence Analysis Data retrieval, De-novo assembly, Read mapping Data retrieval, De-novo assembly, Read mapping Whole genome sequencing, Mapping, Sequence assembly Whole genome sequencing, Mapping, Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vapor /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vapor vapor VAPOR VAPOR is a tool for classification of Influenza samples from raw short read sequence data for downstream bioinformatics analysis. VAPOR is provided with a fasta file of full-length sequences (> 20,000) for a given segment, a set of reads, and attempts to retrieve a reference that is closest to the sample strain. 1 188 188 197466 197466 127 127 1849 1849 0 0 0 0 0 0 0 0 199315 199315 315 315 +vardict_java vardict_java vcf VarDict - calls SNVs and indels for tumour-normal pairs 2020-08-21 https://github.com/AstraZeneca-NGS/VarDictJava 1.8.3 python To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vardict /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vardict 1 48 49 409 424 0 0 0 0 0 0 0 0 0 0 0 0 424 409 49 48 +variant_analyzer mut2read, mut2sscs, read2mut fastq, json, xlsx Collection of tools for analyzing variants in duplex consensus sequencing (DCS) data 2019-11-20 2.0.0 matplotlib To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/variant_analyzer /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/variant_analyzer 3 5 6 54 99 26 29 221 557 0 0 0 0 0 0 0 0 656 275 35 31 +varscan varscan_copynumber, varscan_mpileup, varscan_somatic interval, vcf VarScan is a variant caller for high-throughput sequencing data 2018-07-10 https://dkoboldt.github.io/varscan/ 2.4.3 varscan 2.4.6 To update Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varscan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/varscan 3 813 965 13818 16510 2269 2508 18111 19895 101 101 1552 1552 288 288 1010 1010 38967 34491 3862 3471 +varvamp varvamp txt, fasta, bed, tabular, pdf Variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses 2024-01-27 https://github.com/jonas-fuchs/varVAMP/ 1.3 varvamp 1.3.2 To update Sequence Analysis PCR primer design PCR primer design Virology, Probes and primers Virology, Probes and primers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/varvamp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/varvamp varvamp varVAMP variable VirusAMPlicons (varVAMP) is a tool to design primers for highly diverse viruses. The input is an alignment of your viral (full-genome) sequences. 1 55 55 912 912 0 0 0 0 0 0 0 0 0 0 0 0 912 912 55 55 +vcf2maf vcf2maf tabular vcf2maf: Convert VCF into MAF 2022-06-28 https://github.com/mskcc/vcf2maf @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ vcf2maf 1.6.22 To update Convert Formats iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcf2maf /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vcf2maf 1 64 64 1688 1688 0 0 0 0 7 7 179 179 0 0 0 0 1867 1867 71 71 +vcf2tsv vcf2tsv tabular Converts VCF files into tab-delimited format 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis, Convert Formats devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcf2tsv /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcf2tsv 1 1000 1110 178652 180838 1122 2888 17000 45505 165 203 4866 5129 72 73 252 254 231726 200770 4274 2359 +vcfaddinfo vcfaddinfo vcf Adds info fields from the second dataset which are not present in the first dataset. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfaddinfo /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfaddinfo 1 26 32 858 1007 36 118 6132 9104 7 7 184 237 0 0 0 0 10348 7174 157 69 +vcfallelicprimitives vcfallelicprimitives vcf Splits alleleic primitives (gaps or mismatches) into multiple VCF lines 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfallelicprimitives /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfallelicprimitives 1 918 1372 7607 21544 1134 2095 6447 15257 234 280 3141 3515 4 6 4 8 40324 17199 3753 2290 +vcfanno vcfanno vcf Annotate VCF files 2021-01-17 https://github.com/brentp/vcfanno 0.3.9 vcfanno 0.3.9 Up-to-date Variant Analysis SNP annotation SNP annotation Genetic variation, Data submission, annotation and curation Genetic variation, Data submission, annotation and curation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcfanno /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vcfanno vcfanno vcfanno Fast, flexible annotation of genetic variants. 1 239 239 1308 1308 0 0 0 0 0 0 0 0 0 0 0 0 1308 1308 239 239 +vcfannotate vcfannotate vcf Intersect VCF records with BED annotations 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotate /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfannotate 1 161 206 2810 3070 627 1507 3510 14904 61 69 604 730 5 6 13 14 18718 6937 1788 854 +vcfannotategenotypes vcfannotategenotypes vcf Annotate genotypes in a VCF dataset using genotypes from another VCF dataset. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfannotategenotypes /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfannotategenotypes 1 57 73 114 218 133 403 404 1863 13 13 199 253 1 1 3 3 2337 720 490 204 +vcfbedintersect vcfbedintersect vcf Intersect VCF and BED datasets 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbedintersect /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfbedintersect 1 208 251 3039 4433 423 1241 4483 21130 42 47 546 658 2 3 17 22 26243 8085 1542 675 +vcfbreakcreatemulti vcfbreakcreatemulti vcf Break multiple alleles into multiple records, or combine overallpoing alleles into a single record 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfbreakcreatemulti /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfbreakcreatemulti 1 29 40 265 478 61 320 3591 10654 7 8 386 485 0 1 0 1 11618 4242 369 97 +vcfcheck vcfcheck vcf Verify that the reference allele matches the reference genome 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcheck /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfcheck 1 109 128 1560 1680 207 669 754 2025 18 19 401 461 1 1 1 1 4167 2716 817 335 +vcfcombine vcfcombine vcf Combine multiple VCF datasets 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcombine /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfcombine 1 337 585 1639 2560 996 2856 4286 20198 59 74 481 585 6 6 13 13 23356 6419 3521 1398 +vcfcommonsamples vcfcommonsamples vcf Output records belonging to samples commong between two datasets. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfcommonsamples /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfcommonsamples 1 36 49 81 270 78 297 211 1889 10 13 217 282 3 3 15 15 2456 524 362 127 +vcfdistance vcfdistance vcf Calculate distance to the nearest variant. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfdistance /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfdistance 1 96 106 520 648 135 322 1960 2480 21 24 303 368 2 2 2 2 3498 2785 454 254 +vcffilter vcffilter2 vcf Tool for filtering VCF files 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffilter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcffilter 1 2682 2972 41687 54337 5382 11813 62117 173095 319 406 3130 3934 53 53 266 266 231632 107200 15244 8436 +vcffixup vcffixup vcf Count the allele frequencies across alleles present in each record in the VCF file. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcffixup /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcffixup 1 177 208 1003 1179 282 1037 2113 5539 26 34 252 322 1 1 1 1 7041 3369 1280 486 +vcfflatten vcfflatten2 vcf Removes multi-allelic sites by picking the most common alternate 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfflatten /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfflatten 1 24 32 67 194 68 218 360 988 12 16 193 393 1 1 50 50 1625 670 267 105 +vcfgeno2haplo vcfgeno2haplo vcf Convert genotype-based phased alleles into haplotype alleles 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgeno2haplo /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfgeno2haplo 1 117 134 791 900 192 549 2408 3817 22 26 243 308 2 2 4 4 5029 3446 711 333 +vcfgenotypes vcfgenotypes tabular Convert numerical representation of genotypes to allelic. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfgenotypes /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfgenotypes 1 142 171 1337 1568 246 900 3621 6730 23 26 231 291 1 1 6 6 8595 5195 1098 412 +vcfhethom vcfhethom tabular Count the number of heterozygotes and alleles, compute het/hom ratio. 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfhethom /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfhethom 1 261 279 2002 2396 183 682 1967 4292 19 27 584 754 3 3 12 12 7454 4565 991 466 +vcfleftalign vcfleftalign vcf Left-align indels and complex variants in VCF dataset 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfleftalign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfleftalign 1 42 52 616 740 85 301 345 1145 9 16 188 270 1 2 1 2 2157 1150 371 137 +vcfprimers vcfprimers fasta Extract flanking sequences for each VCF record 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfprimers /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfprimers 1 29 39 450 722 68 215 324 880 10 13 197 267 1 1 3 3 1872 974 268 108 +vcfrandomsample vcfrandomsample vcf Randomly sample sites from VCF dataset 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfrandomsample /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfrandomsample 1 17 20 89 186 27 81 111 361 6 6 194 243 0 0 0 0 790 394 107 50 +vcfselectsamples vcfselectsamples vcf Select samples from a VCF file 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfselectsamples /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfselectsamples 1 77 102 786 973 179 989 923 6360 22 24 349 427 0 0 0 0 7760 2058 1115 278 +vcfsort vcfsort vcf Sort VCF dataset by coordinate 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfsort /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfsort 1 209 236 1958 2132 413 1369 12476 25718 79 89 597 785 4 4 74 74 28709 15105 1698 705 +vcfvcfintersect vcfvcfintersect vcf Intersect two VCF datasets 2017-01-24 https://github.com/ekg/vcflib @WRAPPER_VERSION@ vcflib 1.0.15 To update Variant Analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tool_collections/vcflib/vcfvcfintersect /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tool_collections/vcflib/vcfvcfintersect 1 768 874 977198 979857 916 2249 64595 84741 232 244 18029 21296 15 16 1681 1682 1087576 1061503 3383 1931 +vcontact2 vcontact2, vcontact2_gene2genome csv, tabular Tool to provide taxonomic context of metagenomic sequencing data 2025-11-10 https://bitbucket.org/MAVERICLab/vcontact2/src/master/ 0.11.3 python To update Metagenomics Deposition, Taxonomic classification, Genome annotation Deposition, Taxonomic classification, Genome annotation Taxonomy, Metagenomics, Microbial ecology Taxonomy, Metagenomics, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vcontact2 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vcontact2 vConTACT vConTACT Network-based application utilizing whole genome gene-sharing profiles for virus taxonomy that integrates distance-based hierarchical clustering and confidence scores for all taxonomic predictions. 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +vegan vegan_diversity, vegan_fisher_alpha, vegan_rarefaction tabular, png, txt an R package fo community ecologist 2015-08-27 https://cran.r-project.org/package=vegan 2.4-3 r-vegan 2.3_4 To update Metagenomics Standardisation and normalisation, Analysis Standardisation and normalisation, Analysis Ecology, Phylogenetics, Environmental science Ecology, Phylogenetics, Environmental science iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vegan /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vegan vegan vegan Ordination methods, diversity analysis and other functions for community and vegetation ecologists 3 101 116 2314 2547 167 318 3493 5788 0 0 0 0 0 0 0 0 8335 5807 434 268 +velocyto velocyto_cli loom, txt Velocyto is a library for the analysis of RNA velocity. 2021-04-30 http://velocyto.org/ 0.17.17 velocyto.py 0.17.17 Up-to-date Transcriptomics, Single Cell RNA-Seq analysis, Splicing analysis RNA-Seq analysis, Splicing analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/velocyto /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/velocyto velocyto Velocyto Estimating RNA velocity in single cell RNA sequencing datasets 1 14 14 131 131 12 12 75 75 1 1 192 192 0 0 0 0 398 398 27 27 +velvet velvetg, velveth txt, afg, fasta, tabular, velvet de novo genomic assembler specially designed for short read sequencing technologies 2020-06-09 https://www.ebi.ac.uk/~zerbino/velvet/ @WRAPPER_VERSION@.3 velvet 1.2.10 To update Assembly Formatting, De-novo assembly Formatting, De-novo assembly Sequence assembly Sequence assembly devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/velvet velvet Velvet A de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454 or SOLiD. 2 2567 2888 27621 32158 4951 5263 52855 57273 2097 2221 30746 33121 109 109 1097 1097 123649 112319 10481 9724 +velvetoptimiser velvetoptimiser fasta, tabular Automatically optimize Velvet assemblies 2017-12-19 2.2.6 velvet 1.2.10 To update Assembly Optimisation and refinement, Sequence assembly Optimisation and refinement, Sequence assembly Genomics, Sequence assembly Genomics, Sequence assembly simon-gladman https://github.com/galaxyproject/tools-iuc/tree/main/tools/velvet_optimiser /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/velvet_optimiser velvetoptimiser VelvetOptimiser This tool is designed to run as a wrapper script for the Velvet assembler (Daniel Zerbino, EBI UK) and to assist with optimising the assembly. 1 968 1161 4741 6009 2238 2532 9434 10734 849 1433 2848 5743 0 0 0 0 22486 17023 5126 4055 +verkko verkko fasta, tabular, gfa1, fasta.gz Telomere-to-telomere assembly pipeline 2023-01-24 https://github.com/marbl/verkko @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ verkko 2.3.2 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/verkko /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/verkko 1 43 43 105 105 0 0 0 0 13 13 136 136 0 0 0 0 241 241 56 56 +vg vg_convert, vg_deconstruct, vg_view odgi, vcf, vg Variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods 2020-04-08 https://github.com/vgteam/vg 1.23.0 vg 1.73.0 To update Sequence Analysis, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vg /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vg 3 12 15 15 480 0 0 0 0 0 0 0 0 0 0 0 0 480 15 15 12 +vgp-processcuration vgp_chromosome_assignment, vgp_sak_generation, vgp_split_agp tabular, fasta vgp_processcuration toolkit wrappers 2025-12-19 https://github.com/vgl-hub/vgl-curation 1.1 vgp-processcuration 1.1 Up-to-date Assembly Sequence assembly Sequence assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vgp_processcuration /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vgp_processcuration vgp-processcuration Process Curation ProcessCurated is a set of tools to process curated genome assemblies. In combination with gfastats and mashmap, it reconciliates the AGP file manually curated in PretextView to rename, reorient, and sort the assemblies to get them ready for submission. 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +viralverify viralverify fasta, csv, txt, genbank Contigs prediction as viral, chromosomal, plasmidic or uncertain. 2025-07-04 https://github.com/ablab/viralVerify @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ viralverify 1.1 To update Sequence Analysis, Metagenomics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/viralverify /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/viralverify 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +virannot virannot_blast2tsv, virannot_otu, virAnnot_rps2tsv tabular, xlsx, zip virAnnot wrappers 2025-08-04 https://github.com/marieBvr/virAnnot 1.2.0 biopython 1.70 To update Metagenomics Sequence annotation, Sequence clustering, Sequence cluster visualisation Sequence annotation, Sequence clustering, Sequence cluster visualisation Metagenomics, Virology, Microbial ecology Metagenomics, Virology, Microbial ecology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virannot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/virannot virannot virAnnot "VirAnnot was build to ease the assembly, blast search, taxonomic annotation and OTUs assignation of viral metagenomic HTS data. It is used in Virologie team of UMR1332 BFP laboratory at INRAE. VirAnnot also takes part of the Euphresco project ""Plant Health Bioinformatics Network"". See more.It is designed to identify viruses in plant metagenomic data but it can be used to assemble and annotate any sequences with the NCBI taxonomy." 3 16 16 336 336 0 0 0 0 0 0 0 0 2 2 14 14 350 350 18 18 +virheat virheat pdf generates a heatmap of allele frequencies from vcf files 2024-05-15 https://github.com/jonas-fuchs/virHEAT 0.7.1 virheat 0.7.6 To update Visualization, Variant Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virheat /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/virheat virheat virHEAT VirHEAT tool generates multi-sample variant-frequency plots from SnpEff-annotated viral variant lists. The tool provides a condensed look at variant frequencies after mapping raw reads to a viral/bacterial reference genome and compares multiple vcf files at the same time. 1 7 7 29 29 0 0 0 0 0 0 0 0 0 0 0 0 29 29 7 7 +virhunter virhunter tabular, fasta Deep Learning method for novel virus detection in sequencing data 2022-09-13 https://github.com/cbib/virhunter 1.0.0 numpy To update Machine Learning Sequence classification Sequence classification Virology Virology iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virhunter /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/virhunter virhunter VirHunter VirHunter is a deep learning method that uses Convolutional Neural Networks (CNNs) and a Random Forest Classifier to identify viruses in sequencing datasets. More precisely, VirHunter classifies previously assembled contigs as viral, host, and bacterial (contamination). 1 121 121 1700 1700 0 0 0 0 0 0 0 0 0 0 0 0 1700 1700 121 121 +virulign virulign txt A tool for codon-correct pairwise alignments, with an augmented functionality to annotate the alignment according the positions of the proteins. 2025-08-14 https://github.com/rega-cev/virulign @TOOL_VERSION@+galaxy@VERSION_SUFFIX@ virulign 1.1.1 To update RNA, Sequence Analysis, Fasta Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/virulign /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/virulign 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +volcanoplot volcanoplot pdf, txt Tool to create a Volcano Plot 2018-10-01 https://ggplot2.tidyverse.org/ @TOOL_VERSION@ r-ggplot2 2.2.1 To update Visualization, Transcriptomics, Statistics iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/volcanoplot /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/volcanoplot https://usegalaxy.eu/published/workflow?id=04df470a38b10e94, https://usegalaxy.eu/published/workflow?id=95c4d5549e820d88, https://usegalaxy.eu/published/workflow?id=a9469155eee12ff1, https://usegalaxy.eu/published/workflow?id=c3a11e1ac1aa8383, https://usegalaxy.eu/published/workflow?id=c7b9fb6872444809 1 4591 5038 38589 45177 6962 7279 66385 70667 1001 1068 8606 9348 266 267 1555 1558 126750 115135 13652 12820 +vsearch vsearch_alignment, vsearch_chimera_detection, vsearch_clustering, vsearch_dereplication, vsearch_masking, vsearch_search, vsearch_shuffling, vsearch_sorting fasta, tabular VSEARCH including searching, clustering, chimera detection, dereplication, sorting, masking and shuffling of sequences. 2014-11-30 https://github.com/torognes/vsearch 2.8.3 vsearch 2.31.0 To update Sequence Analysis DNA mapping, Chimera detection DNA mapping, Chimera detection Metagenomics, Sequence analysis Metagenomics, Sequence analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsearch /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vsearch vsearch VSEARCH High-throughput search and clustering sequence analysis tool. It supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering and conversion. 8 226 259 13600 15795 323 642 14828 59476 82 97 6641 7811 11 12 285 286 83368 35354 1010 642 +vsnp vsnp_add_zero_coverage, vsnp_build_tables, vsnp_determine_ref_from_data, vsnp_get_snps, vsnp_statistics vcf, tabular, txt, html The vSNP tools are critical components of several workflows that validate SNPs and produce annotatedSNP tables and corresponding phylogenetic trees. 2020-04-26 https://github.com/USDA-VS/vSNP 3.0.6 pysam 0.24.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/vsnp /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/vsnp 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +weblogo3 rgweblogo3 pdf Sequence Logo generator for fasta 2017-11-17 3.5.0 weblogo 3.7.9 To update Graphics Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Sequence cluster visualisation, Sequence visualisation, Sequence motif recognition Nucleic acid sites, features and motifs, Sequence analysis Nucleic acid sites, features and motifs, Sequence analysis devteam https://github.com/galaxyproject/tools-iuc/tree/main/tools/weblogo3 /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/weblogo3 weblogo WebLogo Web-based application designed to make generate sequence logos. 1 305 344 3638 3856 1198 3777 8383 31758 52 69 577 1423 10 10 40 40 37077 12638 4200 1565 +wfmash wfmash paf wfmash is an aligner for pangenomes that combines efficient homology mapping with base-level alignment. wfmash is the key algorithm in pggb (the PanGenome Graph Builder), where it is applied to make an all-to-all alignment of input genomes that defines the base structure of the pangenome graph. It can scale to support the all-to-all alignment of hundreds of human genomes. 2026-02-09 https://github.com/waveygang/wfmash 0.14.0 wfmash 0.24.2 To update Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/wfmash /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/wfmash 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 +windowmasker windowmasker_mkcounts, windowmasker_ustat txt, bed Identify repetitive regions using WindowMasker 2023-12-14 https://www.ncbi.nlm.nih.gov/IEB/ToolBox/CPP_DOC/lxr/source/src/app/winmasker/ 1.0 blast 2.17.0 To update Sequence Analysis iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/windowmasker /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/windowmasker 2 23 23 856 856 14 14 609 609 3 3 807 807 0 0 0 0 2272 2272 40 40 +winnowmap winnowmap bam A long-read mapping tool optimized for mapping ONT and PacBio reads to repetitive reference sequences. 2021-04-29 https://github.com/marbl/Winnowmap 2.03 winnowmap 2.03 Up-to-date Next Gen Mappers iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/winnowmap /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/winnowmap 1 54 54 317 317 19 19 90 90 0 0 0 0 0 0 0 0 407 407 73 73 +xpath xpath xml XPath XML querying tool 2015-04-14 http://search.cpan.org/dist/XML-XPath/ @WRAPPER_VERSION@.0 perl-xml-xpath 1.47 To update Text Manipulation iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/xpath /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/xpath 1 8 10 30 248 0 1 0 1 0 0 0 0 0 0 0 0 249 30 11 8 +yahs yahs agp, fasta, txt Yet Another Hi-C scaffolding tool 2022-06-28 https://github.com/c-zhou/yahs @VERSION@+galaxy@VERSION_SUFFIX@ yahs 1.2.2 To update Assembly iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/yahs /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/yahs 1 291 291 2516 2516 107 107 750 750 41 41 1062 1062 0 0 0 0 4328 4328 439 439 +zerone zerone interval ChIP-seq discretization and quality control 2018-09-05 https://github.com/nanakiksc/zerone 1.0 zerone 1.0 Up-to-date ChIP-seq iuc https://github.com/galaxyproject/tools-iuc/tree/main/tools/zerone /home/paul-zierep/.galaxy_tool_repos/galaxyproject-tools-iuc/tools/zerone 1 7 12 14 96 0 0 0 0 0 0 0 0 0 0 0 0 96 14 12 7 diff --git a/sources/README.md b/sources/README.md index ef3e37333..9c46b28c6 100644 --- a/sources/README.md +++ b/sources/README.md @@ -84,20 +84,36 @@ A GitHub action performs every week the following steps: ## Extract all tools outside a GitHub Action -1. Get an API key ([personal token](https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/managing-your-personal-access-tokens)) for GitHub -2. Export the GitHub API key as an environment variable: +Tool repositories are cloned locally from the [planemo-monitor](https://github.com/galaxyproject/planemo-monitor) list and extracted without needing a GitHub API token. Repositories are cached in `~/.galaxy_tool_repos` and updated incrementally on subsequent runs. - ``` - $ export GITHUB_API_KEY= - ``` +Run the script to extract all tools: -3. Run the script to extract all tools +``` +$ bash sources/bin/extract_all_tools.sh +``` - ``` - $ bash sources/bin/extract_all_tools.sh - ``` +Additional options can be passed directly to the Python script: + +``` +$ python sources/bin/extract_galaxy_tools.py extract \ + --all output.json \ + --all-tsv output.tsv \ + --all-yml output.yml \ + --all-workflows communities/all/resources/workflows.json \ + --all-tutorials communities/all/resources/tutorials.json \ + --repo-dir ~/.galaxy_tool_repos \ + --workers 4 +``` + +Options: +- `--repo-dir` — Directory to clone repositories into (default: `~/.galaxy_tool_repos`) +- `--repo-url` — Process only specific repo URL(s) (can be specified multiple times, overrides planemo-monitor list) +- `--workers N` — Number of parallel workers for tool parsing (default: 1, sequential) +- `--clone-depth N` — Git clone depth (default: 1 for shallow/CI-friendly; pass `0` for full git history including accurate first-commit dates) +- `--planemo-repository-list` — Process only a specific planemo-monitor list file (e.g., `repositories01.list`) +- `--test` — Run on a small test repository instead of the full list -The script will generate a TSV file with each tool found in the list of GitHub repositories and metadata for these tools: +The script will generate a TSV file with each tool found in the list of tool repositories and metadata for these tools: 1. Galaxy wrapper id 2. Description diff --git a/sources/bin/extract_all_tools.sh b/sources/bin/extract_all_tools.sh index ab04b88f0..298ee43cb 100755 --- a/sources/bin/extract_all_tools.sh +++ b/sources/bin/extract_all_tools.sh @@ -7,14 +7,14 @@ then echo "Test tool extraction" python sources/bin/extract_galaxy_tools.py \ extract \ - --api $GITHUB_API_KEY \ --all-tsv "communities/all/resources/test_tools.tsv" \ --all "communities/all/resources/test_tools.json" \ --all-workflows "communities/all/resources/test_workflows.json" \ --all-yml 'communities/all/resources/test_tools.yml' \ --all-tutorials "communities/all/resources/test_tutorials.json" \ - --planemo-repository-list "test.list" \ - --test + --test \ + --clone-depth 0 \ + "${@:2}" else tsv_output="communities/all/resources/${1}_tools.tsv" json_output="communities/all/resources/${1}_tools.json" @@ -23,35 +23,35 @@ then if [[ $1 =~ "01" ]]; then python sources/bin/extract_galaxy_tools.py \ extract \ - --api $GITHUB_API_KEY \ --all-tsv $tsv_output \ --all $json_output \ --all-yml $yml_output \ --all-workflows "communities/all/resources/workflows.json" \ --all-tutorials "communities/all/resources/tutorials.json" \ - --planemo-repository-list $1 + --planemo-repository-list $1 \ + --clone-depth 0 else python sources/bin/extract_galaxy_tools.py \ extract \ - --api $GITHUB_API_KEY \ --all-tsv $tsv_output \ --all $json_output \ --all-yml $yml_output \ --all-workflows "communities/all/resources/workflows.json" \ --all-tutorials "communities/all/resources/tutorials.json" \ --planemo-repository-list $1 \ - --avoid-extra-repositories + --avoid-extra-repositories \ + --clone-depth 0 fi fi else echo "Tool extraction" python sources/bin/extract_galaxy_tools.py \ extract \ - --api $GITHUB_API_KEY \ --all-tsv 'communities/all/resources/tools.tsv' \ --all 'communities/all/resources/tools.json' \ --all-yml 'communities/all/resources/tools.yml' \ --all-workflows "communities/all/resources/workflows.json" \ - --all-tutorials "communities/all/resources/tutorials.json" + --all-tutorials "communities/all/resources/tutorials.json" \ + --clone-depth 0 fi diff --git a/sources/bin/extract_galaxy_tools.py b/sources/bin/extract_galaxy_tools.py index 91f80cbc1..425c344d9 100644 --- a/sources/bin/extract_galaxy_tools.py +++ b/sources/bin/extract_galaxy_tools.py @@ -1,12 +1,15 @@ #!/usr/bin/env python import argparse -import base64 import json import re +import subprocess import sys -import time import traceback import xml.etree.ElementTree as et +from concurrent.futures import ( + as_completed, + ThreadPoolExecutor, +) from functools import lru_cache from pathlib import Path from typing import ( @@ -16,6 +19,7 @@ Literal, Optional, Pattern, + Tuple, Union, ) @@ -25,9 +29,6 @@ import shared import yaml from extract_galaxy_workflows import Workflows -from github import Github -from github.ContentFile import ContentFile -from github.Repository import Repository from owlready2 import get_ontology from ruamel.yaml import YAML as ruamelyaml from ruamel.yaml.scalarstring import LiteralScalarString @@ -120,90 +121,426 @@ def get_tool_stats_from_stats_file( return max(relevant_counts) if mode == "max" else sum(relevant_counts) -def get_string_content(cf: ContentFile) -> str: - """ - Get string of the content from a ContentFile - - :param cf: GitHub ContentFile object - """ - - return base64.b64decode(cf.content).decode("utf-8") - - -def get_tool_github_repositories( - g: Github, - repository_list: Optional[str], - run_test: bool, +def get_tool_repositories( + clone_dir: Path, + repository_list: Optional[str] = None, + run_test: bool = False, test_repository: str = "https://github.com/paulzierep/Galaxy-Tool-Metadata-Extractor-Test-Wrapper", add_extra_repositories: bool = True, ) -> List[str]: """ - Get list of tool GitHub repositories to parse + Get list of tool GitHub repositories to parse by cloning planemo-monitor locally. - :param g: GitHub instance - :param repository_list: The selection to use from the repository (needed to split the process for CI jobs) - :param run_test: for testing only parse the repository - :test_repository: the link to the test repository to use for the test + :param clone_dir: directory to clone into + :param repository_list: optional specific .list file to use (for CI splits) + :param run_test: if True, return only the test repository + :param test_repository: URL of the test repository + :param add_extra_repositories: if True, add extra repos from config """ - if run_test: return [test_repository] - repo = g.get_user("galaxyproject").get_repo("planemo-monitor") + planemo_monitor_url = "https://github.com/galaxyproject/planemo-monitor" + dest = clone_dir / "planemo-monitor" + if dest.exists(): + print(f"Updating planemo-monitor in {dest} ...") + subprocess.run(["git", "-C", str(dest), "pull", "--ff-only"], check=False) + else: + dest.parent.mkdir(parents=True, exist_ok=True) + print(f"Cloning planemo-monitor into {dest} ...") + subprocess.run(["git", "clone", "--depth", "1", planemo_monitor_url, str(dest)], check=True) + repo_list: List[str] = [] for i in range(1, 5): - repo_selection = f"repositories0{i}.list" - if repository_list: # only get these repositories - if repository_list == repo_selection: - repo_f = repo.get_contents(repo_selection) - repo_l = get_string_content(repo_f).rstrip() - repo_list.extend(repo_l.split("\n")) - else: - repo_f = repo.get_contents(repo_selection) - repo_l = get_string_content(repo_f).rstrip() - repo_list.extend(repo_l.split("\n")) + list_file = f"repositories0{i}.list" + list_path = dest / list_file + if not list_path.exists(): + continue + if repository_list and repository_list != list_file: + continue + lines = list_path.read_text().splitlines() + for line in lines: + line = line.strip() + if line and not line.startswith("#"): + repo_list.append(line) - if ( - add_extra_repositories and "extra-repositories" in configs - ): # add non planemo monitor repositories defined in conf - repo_list = repo_list + configs["extra-repositories"] + if add_extra_repositories and "extra-repositories" in configs: + repo_list += configs["extra-repositories"] print("Parsing repositories from:") - for repo in repo_list: - print("\t", repo) + for r in repo_list: + print("\t", r) return repo_list -def get_github_repo(url: str, g: Github) -> Repository: - """ - Get a GitHub Repository object from an URL +def _repo_name_from_url(url: str) -> str: + url = url.rstrip("/") + if url.endswith(".git"): + url = url[:-4] + parts = url.split("/") + if len(parts) >= 3: + org = parts[-2] + repo = parts[-1] + return f"{org}-{repo}" + return parts[-1] - :param url: URL to a GitHub repository - :param g: GitHub instance - """ - if not url.startswith("https://github.com/"): - raise ValueError - if url.endswith("/"): - url = url[:-1] + +def _normalize_repo_url(url: str) -> str: + """Normalize a repo URL for deduplication.""" + url = url.strip().rstrip("/") if url.endswith(".git"): url = url[:-4] - u_split = url.split("/") - return g.get_user(u_split[-2]).get_repo(u_split[-1]) + return url -def get_shed_attribute(attrib: str, shed_content: Dict[str, Any], empty_value: Any) -> Any: +def clone_repositories(repo_list: List[str], clone_dir: Path, depth: Optional[int] = 1) -> List[Tuple[str, Path]]: """ - Get a shed attribute + Clone or update GitHub repositories into a local directory. - :param attrib: attribute to extract - :param shed_content: content of the .shed.yml - :param empty_value: value to return if attribute not found + Duplicate URLs are skipped. Uses shallow clones by default for CI efficiency. + + :param repo_list: list of repository URLs + :param clone_dir: directory to clone into + :param depth: git clone depth (None for full history, default 1 for shallow) + :returns: list of (original_url, local_path) tuples """ - if attrib in shed_content: - return shed_content[attrib] + clone_dir.mkdir(parents=True, exist_ok=True) + results: List[Tuple[str, Path]] = [] + seen: set = set() + total = len(repo_list) + for i, url in enumerate(repo_list, 1): + normalized = _normalize_repo_url(url) + if normalized in seen: + print(f" [{i}/{total}] {url} (duplicate, skipped)", flush=True) + continue + seen.add(normalized) + + print(f" [{i}/{total}] {url}", flush=True) + name = _repo_name_from_url(url) + dest = clone_dir / name + if dest.exists(): + subprocess.run(["git", "-C", str(dest), "pull", "--ff-only"]) + else: + clone_cmd = ["git", "clone"] + if depth is not None: + clone_cmd.extend(["--depth", str(depth)]) + clone_cmd.extend([url, str(dest)]) + subprocess.run(clone_cmd) + results.append((url, dest)) + return results + + +def get_first_commit_for_local_folder(repo_path: Path, tool_rel_path: str) -> str: + """ + Get the date of the first commit in the tool folder using git log. + If the clone is shallow, try to fetch more history for the path. + """ + + def _git_log() -> str: + try: + result = subprocess.run( + ["git", "log", "--reverse", "--format=%ad", "--date=short", tool_rel_path], + cwd=repo_path, + capture_output=True, + text=True, + ) + lines = result.stdout.strip().split("\n") + if lines and lines[0]: + return lines[0] + except Exception: + pass + return "" + + date = _git_log() + if not date and (repo_path / ".git" / "shallow").exists(): + try: + subprocess.run( + ["git", "fetch", "--deepen", "1000", "origin"], + cwd=repo_path, + capture_output=True, + text=True, + timeout=120, + ) + date = _git_log() + except Exception: + pass + return date + + +def get_tool_metadata_from_local(tool_path: Path, repo_path: Path, repo_url: str = "") -> Optional[Dict[str, Any]]: + """ + Get tool metadata from a locally cloned tool directory. + Uses Galaxy's xml_macros to expand macros before parsing. + """ + if not tool_path.is_dir(): + return None + + metadata: Dict[str, Any] = { + "Suite ID": None, + "Tool IDs": [], + "Tool output formats": [], + "Description": None, + "Suite first commit date": None, + "Homepage": None, + "Suite version": None, + "Suite conda package": None, + "Latest suite conda package version": None, + "Suite version status": "To update", + "ToolShed categories": [], + "EDAM operations": [], + "EDAM reduced operations": [], + "EDAM topics": [], + "EDAM reduced topics": [], + "Suite owner": None, + "Suite source": None, + "Suite parsed folder": None, + "bio.tool ID": None, + "bio.tool name": None, + "bio.tool description": None, + "biii ID": None, + } + + # extract .shed.yml + shed_path = tool_path / ".shed.yml" + if not shed_path.exists(): + return None + with shed_path.open() as fh: + shed_content = yaml.load(fh, Loader=yaml.FullLoader) + metadata["Description"] = get_shed_attribute("description", shed_content, None) + if metadata["Description"] is None: + metadata["Description"] = get_shed_attribute("long_description", shed_content, None) + if metadata["Description"] is not None: + metadata["Description"] = metadata["Description"].replace("\n", "") + metadata["Suite ID"] = get_shed_attribute("name", shed_content, None) + metadata["Suite owner"] = get_shed_attribute("owner", shed_content, None) + metadata["Suite source"] = get_shed_attribute("remote_repository_url", shed_content, None) + if "homepage_url" in shed_content: + metadata["Homepage"] = shed_content["homepage_url"] + metadata["ToolShed categories"] = get_shed_attribute("categories", shed_content, []) + if metadata["ToolShed categories"] is None: + metadata["ToolShed categories"] = [] + + # build repo URL for parsed folder + tool_rel_path = str(tool_path.relative_to(repo_path)) + if repo_url: + metadata["Suite parsed folder"] = repo_url.rstrip("/") + "/tree/master/" + tool_rel_path else: - return empty_value + metadata["Suite parsed folder"] = str(tool_path) + + # first commit date + metadata["Suite first commit date"] = get_first_commit_for_local_folder(repo_path, tool_rel_path) + + # parse macro files for token values, requirements, xrefs + macro_tokens: Dict[str, str] = {} + for entry in tool_path.iterdir(): + if "macro" in entry.name and entry.name.endswith("xml"): + try: + root = et.fromstring(entry.read_text()) + for child in root: + if "name" in child.attrib: + token_name = child.attrib["name"] + if child.text: + macro_tokens[token_name] = child.text + if token_name in ("@TOOL_VERSION@", "@VERSION@"): + metadata["Suite version"] = child.text + elif token_name == "requirements": + metadata["Suite conda package"] = get_conda_package(child) + biotools = get_xref(child, attrib_type="bio.tools") + if biotools is not None: + metadata["bio.tool ID"] = biotools + biii = get_xref(child, attrib_type="biii") + if biii is not None: + metadata["biii ID"] = biii + except Exception: + print(traceback.format_exc()) + + # resolve macro token values that reference other tokens (multi-pass for chains) + for _ in range(5): + changed = False + for key, val in list(macro_tokens.items()): + resolved = re.sub(r"@(\w+)@", lambda m: macro_tokens.get(m.group(0), m.group(0)), val) + if resolved != val: + macro_tokens[key] = resolved + changed = True + if not changed: + break + + if metadata["Suite version"] is not None and re.search(r"@\w+@", metadata["Suite version"]): + metadata["Suite version"] = re.sub( + r"@(\w+)@", lambda m: macro_tokens.get(m.group(0), m.group(0)), metadata["Suite version"] + ) + + def _resolve_macros(text: str) -> str: + return re.sub(r"@(\w+)@", lambda m: macro_tokens.get(m.group(0), m.group(0)), text) + + # parse each tool XML with macro expansion + for entry in sorted(tool_path.iterdir()): + if entry.name.endswith("xml") and "macro" not in entry.name: + try: + tree = _load_tool_xml_with_macros(entry) + if tree is None: + tree = _load_tool_xml_fallback(entry) + if tree is None: + continue + root = tree.getroot() + except Exception: + print(traceback.format_exc()) + continue + + # version + if metadata["Suite version"] is None and "version" in root.attrib: + raw_version = root.attrib["version"] + metadata["Suite version"] = _resolve_macros(raw_version) + + # bio.tools + biotools = get_xref(root, attrib_type="bio.tools") + if biotools is not None: + metadata["bio.tool ID"] = biotools + + # biii + if metadata["biii ID"] is None: + biii = get_xref(root, attrib_type="biii") + if biii is not None: + metadata["biii ID"] = biii + + # conda package + if metadata["Suite conda package"] is None: + reqs = get_conda_package(root) + if reqs is not None: + metadata["Suite conda package"] = reqs + + # tool ids + if "id" in root.attrib: + metadata["Tool IDs"].append(root.attrib["id"]) + + # tool outputs + formats = get_tool_outputs(root) + for fmt in formats: + if fmt not in metadata["Tool output formats"]: + metadata["Tool output formats"].append(fmt) + + # strip +galaxy suffix from version + if metadata["Suite version"] is not None: + metadata["Suite version"] = re.sub(r"\+galaxy\d+$", "", metadata["Suite version"]) + + # set suite ID fallback + if metadata["Suite ID"] is None: + if metadata["bio.tool ID"] is not None: + metadata["Suite ID"] = metadata["bio.tool ID"].lower() + else: + metadata["Suite ID"] = tool_path.name + + # get latest conda version + if metadata["Suite conda package"] is not None: + r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Suite conda package"]}', timeout=10) + if r.status_code == requests.codes.ok: + conda_info = r.json() + if "latest_version" in conda_info: + metadata["Latest suite conda package version"] = conda_info["latest_version"] + if metadata["Latest suite conda package version"] == metadata["Suite version"]: + metadata["Suite version status"] = "Up-to-date" + + # get bio.tool information + if metadata["bio.tool ID"] is not None: + r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool ID"]}/?format=json', timeout=10) + if r.status_code == requests.codes.ok: + biotool_info = r.json() + if "function" in biotool_info: + for func in biotool_info["function"]: + if "operation" in func: + for op in func["operation"]: + metadata["EDAM operations"].append(op["term"]) + if "topic" in biotool_info: + for t in biotool_info["topic"]: + metadata["EDAM topics"].append(t["term"]) + if "name" in biotool_info: + metadata["bio.tool name"] = biotool_info["name"] + if "description" in biotool_info: + metadata["bio.tool description"] = biotool_info["description"].replace("\n", "") + + return metadata + + +def _load_tool_xml_with_macros(xml_path: Path) -> Optional[Any]: + """Try to load and expand macros using Galaxy's xml_macros (galaxy-util).""" + try: + from galaxy.util.xml_macros import load as _xml_macros_load + + return _xml_macros_load(str(xml_path)) + except Exception: + return None + + +def _load_tool_xml_fallback(xml_path: Path) -> Optional[Any]: + """Fallback: parse XML directly without macro expansion.""" + try: + import xml.etree.ElementTree as _et + + tree = _et.parse(str(xml_path)) + return tree + except Exception: + return None + + +def parse_tools_from_local(repo_path: Path, workers: int = 1, repo_url: str = "") -> List[Dict[str, Any]]: + """ + Parse tools from a locally cloned repository. + """ + tools: List[Dict[str, Any]] = [] + + # look for tool folders in tools/, wrappers/, tool_collections/ + search_dirs = ["tools", "wrappers", "tool_collections"] + found = False + for sd in search_dirs: + candidate = repo_path / sd + if candidate.is_dir(): + found = True + items = [p for p in sorted(candidate.iterdir()) if p.is_dir()] + # collect all tool paths (handle nested .shed.yml) + tool_paths: List[Path] = [] + for item in items: + if (item / ".shed.yml").exists(): + tool_paths.append(item) + else: + for sub in sorted(item.iterdir()): + if sub.is_dir(): + tool_paths.append(sub) + + total = len(tool_paths) + print(f" Parsing {total} tools...", flush=True) + + def _process_one(p: Path) -> Optional[Dict[str, Any]]: + return get_tool_metadata_from_local(p, repo_path, repo_url=repo_url) + + if workers > 1: + with ThreadPoolExecutor(max_workers=workers) as executor: + fut_to_path = {executor.submit(_process_one, p): p for p in tool_paths} + for idx, future in enumerate(as_completed(fut_to_path), 1): + path = fut_to_path[future] + print(f" [{idx}/{total}] {path.name}", flush=True) + try: + metadata = future.result() + if metadata is not None: + tools.append(metadata) + except Exception: + print(f" Error parsing {path.name}", file=sys.stderr) + print(traceback.format_exc()) + else: + for idx, p in enumerate(tool_paths, 1): + print(f" [{idx}/{total}] {p.name}", flush=True) + try: + metadata = _process_one(p) + if metadata is not None: + tools.append(metadata) + except Exception: + print(f" Error parsing {p.name}", file=sys.stderr) + print(traceback.format_exc()) + + if not found: + print("No tool folder found", file=sys.stderr) + + return tools def get_tool_outputs(el: et.Element) -> list[str]: @@ -230,6 +567,20 @@ def get_tool_outputs(el: et.Element) -> list[str]: return formats +def get_shed_attribute(attrib: str, shed_content: Dict[str, Any], empty_value: Any) -> Any: + """ + Get a shed attribute + + :param attrib: attribute to extract + :param shed_content: content of the .shed.yml + :param empty_value: value to return if attribute not found + """ + if attrib in shed_content: + return shed_content[attrib] + else: + return empty_value + + def get_xref(el: et.Element, attrib_type: str) -> Optional[str]: """ Get xref information @@ -287,256 +638,6 @@ def check_categories(ts_categories: str, ts_cat: List[str]) -> bool: return bool(set(ts_cat) & set(ts_cats)) -def get_suite_ID_fallback(metadata: Dict, tool: ContentFile) -> Dict: - """ - Set suite ID fallbacks - - :param metadata: the metadata dict - """ - - # when `name` not in .shed.yml file - if metadata["Suite ID"] is None: - if metadata["bio.tool ID"] is not None: - metadata["Suite ID"] = metadata["bio.tool ID"].lower() - else: - metadata["Suite ID"] = tool.path.split("/")[-1] - - return metadata - - -def get_tool_metadata(tool: ContentFile, repo: Repository) -> Optional[Dict[str, Any]]: - """ - Get tool metadata from the .shed.yaml, requirements in the macros or xml - file, bio.tools information if available in the macros or xml, EDAM - annotations using bio.tools API, recent conda version using conda API - - :param tool: GitHub ContentFile object - :param repo: GitHub Repository object - """ - if tool.type != "dir": - return None - - metadata: dict = { - "Suite ID": None, - "Tool IDs": [], - "Tool output formats": [], - "Description": None, - "Suite first commit date": None, - "Homepage": None, - "Suite version": None, - "Suite conda package": None, - "Latest suite conda package version": None, - "Suite version status": "To update", - "ToolShed categories": [], - "EDAM operations": [], - "EDAM reduced operations": [], - "EDAM topics": [], - "EDAM reduced topics": [], - "Suite owner": None, - "Suite source": None, # this is what it written in the .shed.yml - "Suite parsed folder": None, # this is the actual parsed file - "bio.tool ID": None, - "bio.tool name": None, - "bio.tool description": None, - "biii ID": None, - } - # extract .shed.yml information and check macros.xml - try: - shed = repo.get_contents(f"{tool.path}/.shed.yml") - except Exception: - return None - # parse the .shed.yml - else: - file_content = get_string_content(shed) - yaml_content = yaml.load(file_content, Loader=yaml.FullLoader) - metadata["Description"] = get_shed_attribute("description", yaml_content, None) - if metadata["Description"] is None: - metadata["Description"] = get_shed_attribute("long_description", yaml_content, None) - if metadata["Description"] is not None: - metadata["Description"] = metadata["Description"].replace("\n", "") - metadata["Suite ID"] = get_shed_attribute("name", yaml_content, None) - metadata["Suite owner"] = get_shed_attribute("owner", yaml_content, None) - metadata["Suite source"] = get_shed_attribute("remote_repository_url", yaml_content, None) - if "homepage_url" in yaml_content: - metadata["Homepage"] = yaml_content["homepage_url"] - metadata["ToolShed categories"] = get_shed_attribute("categories", yaml_content, []) - if metadata["ToolShed categories"] is None: - metadata["ToolShed categories"] = [] - - # get all files in the folder - file_list = repo.get_contents(tool.path) - assert isinstance(file_list, list) - - # store the github location where the folder was parsed - metadata["Suite parsed folder"] = tool.html_url - - # get the first commit date - metadata["Suite first commit date"] = shared.get_first_commit_for_folder(tool, repo) - - # find and parse macro file - for file in file_list: - if "macro" in file.name and file.name.endswith("xml"): - file_content = get_string_content(file) - root = et.fromstring(file_content) - for child in root: - if "name" in child.attrib: - if child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@": - metadata["Suite version"] = child.text - elif child.attrib["name"] == "requirements": - metadata["Suite conda package"] = get_conda_package(child) - # bio.tools - biotools = get_xref(child, attrib_type="bio.tools") - if biotools is not None: - metadata["bio.tool ID"] = biotools - # biii - biii = get_xref(child, attrib_type="biii") - if biii is not None: - metadata["biii ID"] = biii - - # parse XML file and get meta data from there - for file in file_list: - if file.name.endswith("xml") and "macro" not in file.name: - try: - file_content = get_string_content(file) - root = et.fromstring(file_content) - except Exception: - print(traceback.format_exc()) - else: - # version - if metadata["Suite version"] is None: - if "version" in root.attrib: - version = root.attrib["version"] - if "VERSION@" not in version: - metadata["Suite version"] = version - else: - macros = root.find("macros") - if macros is not None: - for child in macros: - if "name" in child.attrib and ( - child.attrib["name"] == "@TOOL_VERSION@" or child.attrib["name"] == "@VERSION@" - ): - metadata["Suite version"] = child.text - - # bio.tools - biotools = get_xref(root, attrib_type="bio.tools") - if biotools is not None: - metadata["bio.tool ID"] = biotools - - # biii - if metadata["biii ID"] is None: - biii = get_xref(root, attrib_type="biii") - if biii is not None: - metadata["biii ID"] = biii - - # conda package - if metadata["Suite conda package"] is None: - reqs = get_conda_package(root) - if reqs is not None: - metadata["Suite conda package"] = reqs - - # tool ids - if "id" in root.attrib: - metadata["Tool IDs"].append(root.attrib["id"]) - - # tool outputs - formats = get_tool_outputs(root) - for f in formats: - if f not in metadata["Tool output formats"]: - metadata["Tool output formats"].append(f) - - metadata = get_suite_ID_fallback(metadata, tool) - - # get latest conda version and compare to the wrapper version - if metadata["Suite conda package"] is not None: - r = requests.get(f'https://api.anaconda.org/package/bioconda/{metadata["Suite conda package"]}') - if r.status_code == requests.codes.ok: - conda_info = r.json() - if "latest_version" in conda_info: - metadata["Latest suite conda package version"] = conda_info["latest_version"] - if metadata["Latest suite conda package version"] == metadata["Suite version"]: - metadata["Suite version status"] = "Up-to-date" - - # get bio.tool information - if metadata["bio.tool ID"] is not None: - r = requests.get(f'{BIOTOOLS_API_URL}/api/tool/{metadata["bio.tool ID"]}/?format=json') - if r.status_code == requests.codes.ok: - biotool_info = r.json() - if "function" in biotool_info: - for func in biotool_info["function"]: - if "operation" in func: - for op in func["operation"]: - metadata["EDAM operations"].append(op["term"]) - if "topic" in biotool_info: - for t in biotool_info["topic"]: - metadata["EDAM topics"].append(t["term"]) - if "name" in biotool_info: - metadata["bio.tool name"] = biotool_info["name"] - if "description" in biotool_info: - metadata["bio.tool description"] = biotool_info["description"].replace("\n", "") - return metadata - - -def parse_tools(repo: Repository) -> List[Dict[str, Any]]: - """ - Parse tools in a GitHub repository, extract them and their metadata - - :param repo: GitHub Repository object - """ - # get tool folders - tool_folders: List[List[ContentFile]] = [] - try: - repo_tools = repo.get_contents("tools") - except Exception: - try: - repo_tools = repo.get_contents("wrappers") - except Exception: - print("No tool folder found", sys.stderr) - return [] - assert isinstance(repo_tools, list) - - tool_folders.append(repo_tools) - try: - repo_tools = repo.get_contents("tool_collections") - except Exception: - pass - else: - assert isinstance(repo_tools, list) - tool_folders.append(repo_tools) - - # tool_folders will contain a list of all folders in the - # repository named wrappers/tools/tool_collections - - # parse folders - tools = [] - for folder in tool_folders: - for tool in folder: - # to avoid API request limit issue, wait for one hour - if g.get_rate_limit().resources.core.remaining < 200: - print("WAITING for 1 hour to retrieve GitHub API request access !!!") - print() - time.sleep(60 * 60) - - # parse tool - # if the folder (tool) has a .shed.yml file run get get_tool_metadata on that folder, - # otherwise go one level down and check if there is a .shed.yml in a subfolder - try: - repo.get_contents(f"{tool.path}/.shed.yml") - except Exception: - if tool.type != "dir": - continue - file_list = repo.get_contents(tool.path) - assert isinstance(file_list, list) - for content in file_list: - metadata = get_tool_metadata(content, repo) - if metadata is not None: - tools.append(metadata) - else: - metadata = get_tool_metadata(tool, repo) - if metadata is not None: - tools.append(metadata) - return tools - - @lru_cache # need to run this for each suite, so just cache it def get_all_installed_tool_ids_on_server(galaxy_url: str) -> List[str]: """ @@ -548,7 +649,7 @@ def get_all_installed_tool_ids_on_server(galaxy_url: str) -> List[str]: base_url = f"{galaxy_url}/api" try: - r = requests.get(f"{base_url}/tools", params={"in_panel": False}) + r = requests.get(f"{base_url}/tools", params={"in_panel": False}, timeout=30) r.raise_for_status() tool_dict_list = r.json() tools = [tool_dict["id"] for tool_dict in tool_dict_list] @@ -757,73 +858,6 @@ def aggregate_tool_stats( return tool -def get_tools( - repo_list: list, all_workflows: str = "", all_tutorials: str = "", edam_ontology: Optional[Dict] = None -) -> List[Dict]: - """ - Parse tools in GitHub repositories to extract metadata, - filter by TS categories, additional information - """ - tools: List[Dict] = [] - for r in repo_list: - print("Parsing tools from:", (r)) - if "github" not in r: - continue - try: - repo = get_github_repo(r, g) - tools.extend(parse_tools(repo)) - except Exception as e: - print( - f"Error while extracting tools from repo {r}: {e}", - file=sys.stderr, - ) - print(traceback.format_exc()) - - # add additional information to tools - for tool in tools: - # add EDAM terms without superclass - tool["EDAM reduced operations"] = reduce_ontology_terms(tool["EDAM operations"], ontology=edam_ontology) - tool["EDAM reduced topics"] = reduce_ontology_terms(tool["EDAM topics"], ontology=edam_ontology) - - # add availability for UseGalaxy servers - for name, url in USEGALAXY_SERVER_URLS.items(): - tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) - - # add all other available servers - public_servers_df = pd.read_csv(public_servers, sep="\t") - for _index, row in public_servers_df.iterrows(): - name = row["name"] - - if name.lower() not in [ - n.lower() for n in USEGALAXY_SERVER_URLS.keys() - ]: # do not query UseGalaxy servers again - - url = row["url"] - tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) - - # add tool stats - for name, path in GALAXY_TOOL_STATS.items(): - tool_stats_df = pd.read_csv(path) - - # we take the max for suite users being conservative, since one user can use multiple tools - # in the suite - mode: Literal["sum", "max"] - if "Suite users" in name: - mode = "max" - else: - mode = "sum" - - tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Tool IDs"], mode=mode) - - # sum up tool stats - tool = aggregate_tool_stats(tool, STATS_SUM) - - tools = add_workflow_ids_to_tools(tools, all_workflows) - tools = add_tutorial_ids_to_tools(tools, all_tutorials) - - return tools - - def add_workflow_ids_to_tools(tools: List[Dict[str, Any]], all_workflows: str) -> List[Dict[str, Any]]: """ Add related workflow links to the tools dict. @@ -1098,7 +1132,6 @@ def export_tools_to_yml(tools: List[Dict], yml_output_path: str) -> None: subparser = parser.add_subparsers(dest="command") # Extract tools extract = subparser.add_parser("extract", help="Extract tools") - extract.add_argument("--api", "-a", required=True, help="GitHub access token") extract.add_argument("--all", "-o", required=True, help="Filepath to JSON with all extracted tools") extract.add_argument("--all-tsv", "-j", required=True, help="Filepath to TSV with all extracted tools") extract.add_argument("--all-yml", "-y", required=True, help="Filepath to yml with all extracted tools") @@ -1136,6 +1169,30 @@ def export_tools_to_yml(tools: List[Dict], yml_output_path: str) -> None: required=False, help="Run a small test case using only the repository: https://github.com/TGAC/earlham-galaxytools", ) + extract.add_argument( + "--repo-dir", + default="~/.galaxy_tool_repos", + help="Directory to clone repositories into (default: ~/.galaxy_tool_repos)", + ) + extract.add_argument( + "--repo-url", + action="append", + dest="repo_urls", + default=None, + help="Specific repo URL(s) to process (can be specified multiple times). Overrides planemo-monitor list.", + ) + extract.add_argument( + "--workers", + type=int, + default=1, + help="Number of parallel workers for tool parsing (default: 1, sequential)", + ) + extract.add_argument( + "--clone-depth", + type=int, + default=None, + help="Git clone depth for tool repositories (default: shallow=1; 0 for full history)", + ) # Filter tools based on ToolShed categories filtertools = subparser.add_parser("filter", help="Filter tools based on ToolShed categories") @@ -1224,18 +1281,67 @@ def export_tools_to_yml(tools: List[Dict], yml_output_path: str) -> None: args = parser.parse_args() if args.command == "extract": - # connect to GitHub - g = Github(args.api) - # get list of GitHub repositories to parse - repo_list = get_tool_github_repositories( - g=g, - repository_list=args.planemo_repository_list, - run_test=args.test, - add_extra_repositories=not args.avoid_extra_repositories, - ) - # parse tools in GitHub repositories to extract metadata, filter by TS categories and export to output file + repo_dir = Path(args.repo_dir).expanduser() + if args.repo_urls: + repo_list = args.repo_urls + print("Using specified repositories:") + for r in repo_list: + print("\t", r) + elif args.test: + repo_list = get_tool_repositories( + clone_dir=repo_dir, + run_test=True, + add_extra_repositories=False, + ) + else: + repo_list = get_tool_repositories( + clone_dir=repo_dir, + repository_list=args.planemo_repository_list, + add_extra_repositories=not args.avoid_extra_repositories, + ) + edam_ontology = get_ontology("https://edamontology.org/EDAM_1.25.owl").load() - tools = get_tools(repo_list, args.all_workflows, args.all_tutorials, edam_ontology) + + print(f"Cloning repositories into {repo_dir} ...") + clone_depth = None if args.clone_depth == 0 else (args.clone_depth or 1) + cloned = clone_repositories(repo_list, repo_dir, depth=clone_depth) + tools: List[Dict] = [] + for url, repo_path in cloned: + print(f"Parsing tools from: {url} ({repo_path})") + tools.extend(parse_tools_from_local(repo_path, workers=args.workers, repo_url=url)) + if args.all_workflows: + tools = add_workflow_ids_to_tools(tools, args.all_workflows) + if args.all_tutorials: + tools = add_tutorial_ids_to_tools(tools, args.all_tutorials) + for tool in tools: + tool.setdefault("Related Workflows", []) + tool.setdefault("Related Tutorials", []) + for tool in tools: + tool["EDAM reduced operations"] = reduce_ontology_terms(tool["EDAM operations"], ontology=edam_ontology) + tool["EDAM reduced topics"] = reduce_ontology_terms(tool["EDAM topics"], ontology=edam_ontology) + if args.test: + tool["Number of tools on UseGalaxy.eu"] = check_tools_on_servers( + tool["Tool IDs"], USEGALAXY_SERVER_URLS["UseGalaxy.eu"] + ) + else: + for name, url in USEGALAXY_SERVER_URLS.items(): + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) + public_servers_df = pd.read_csv(public_servers, sep="\t") + for _index, row in public_servers_df.iterrows(): + name = row["name"] + if name.lower() not in [n.lower() for n in USEGALAXY_SERVER_URLS.keys()]: + url = row["url"] + tool[f"Number of tools on {name}"] = check_tools_on_servers(tool["Tool IDs"], url) + for name, path in GALAXY_TOOL_STATS.items(): + tool_stats_df = pd.read_csv(path) + mode: Literal["sum", "max"] + if "Suite users" in name: + mode = "max" + else: + mode = "sum" + tool[name] = get_tool_stats_from_stats_file(tool_stats_df, tool["Tool IDs"], mode=mode) + tool = aggregate_tool_stats(tool, STATS_SUM) + export_tools_to_json(tools, args.all) export_tools_to_tsv(tools, args.all_tsv, format_list_col=True) export_tools_to_yml(tools, args.all_yml) diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/.shed.yml b/sources/bin/tests/test-data/2d_auto_threshold_test/.shed.yml new file mode 100644 index 000000000..fac77027c --- /dev/null +++ b/sources/bin/tests/test-data/2d_auto_threshold_test/.shed.yml @@ -0,0 +1,8 @@ +categories: + - Imaging +description: Automatic thresholding +long_description: Applying a standard thresholding method to an image. +name: 2d_auto_threshold +owner: imgteam +homepage_url: https://github.com/bmcv +remote_repository_url: https://github.com/BMCV/galaxy-image-analysis/tree/master/tools/2d_auto_threshold/ diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.py b/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.py new file mode 100644 index 000000000..c2fd832d5 --- /dev/null +++ b/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.py @@ -0,0 +1,48 @@ +""" +Copyright 2017-2022 Biomedical Computer Vision Group, Heidelberg University. + +Distributed under the MIT license. +See file LICENSE for detail or copy at https://opensource.org/licenses/MIT + +""" + +import argparse + +import skimage.filters +import skimage.io +import skimage.util +import tifffile + +thOptions = { + "otsu": lambda img_raw, bz: skimage.filters.threshold_otsu(img_raw), + "li": lambda img_raw, bz: skimage.filters.threshold_li(img_raw), + "yen": lambda img_raw, bz: skimage.filters.threshold_yen(img_raw), + "isodata": lambda img_raw, bz: skimage.filters.threshold_isodata(img_raw), + "loc_gaussian": lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method="gaussian"), + "loc_median": lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method="median"), + "loc_mean": lambda img_raw, bz: skimage.filters.threshold_local(img_raw, bz, method="mean"), +} + + +def auto_thresholding(in_fn, out_fn, th_method, block_size=5, dark_bg=True): # type: ignore[no-untyped-def] + img = skimage.io.imread(in_fn) + th = thOptions[th_method](img, block_size) + if dark_bg: + res = img > th + else: + res = img <= th + tifffile.imwrite(out_fn, skimage.util.img_as_ubyte(res)) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser(description="Automatic Image Thresholding") + parser.add_argument("im_in", help="Path to the input image") + parser.add_argument("im_out", help="Path to the output image (TIFF)") + parser.add_argument("th_method", choices=thOptions.keys(), help="Thresholding method") + parser.add_argument( + "block_size", type=int, default=5, help="Odd size of pixel neighborhood for calculating the threshold" + ) + parser.add_argument("dark_bg", default=True, type=bool, help="True if background is dark") + args = parser.parse_args() + + auto_thresholding(args.im_in, args.im_out, args.th_method, args.block_size, args.dark_bg) diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.xml b/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.xml new file mode 100644 index 000000000..b4efa7c46 --- /dev/null +++ b/sources/bin/tests/test-data/2d_auto_threshold_test/auto_threshold.xml @@ -0,0 +1,63 @@ + + with scikit-image + + operation_3443 + + + scikit-image + scikit-image + + + scikit-image + tifffile + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + Applies a standard thresholding algorithm to an image. + + + 10.1016/j.jbiotec.2017.07.019 + + diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out.tif b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out.tif new file mode 100644 index 000000000..cdd6ea03b Binary files /dev/null and b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out.tif differ diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out2.tif b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out2.tif new file mode 100644 index 000000000..85c97d2ca Binary files /dev/null and b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/out2.tif differ diff --git a/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/sample.tif b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/sample.tif new file mode 100644 index 000000000..0d1b003b4 Binary files /dev/null and b/sources/bin/tests/test-data/2d_auto_threshold_test/test-data/sample.tif differ diff --git a/sources/bin/tests/test-data/fastp_test/.shed.yml b/sources/bin/tests/test-data/fastp_test/.shed.yml new file mode 100644 index 000000000..42f252862 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/.shed.yml @@ -0,0 +1,10 @@ +categories: +- Sequence Analysis +description: Fast all-in-one preprocessing for FASTQ files +homepage_url: https://github.com/OpenGene/fastp +long_description: | + A tool designed to provide fast all-in-one preprocessing for FASTQ files. This tool is developed in C++ with multithreading supported to afford high performance. +remote_repository_url: https://github.com/galaxyproject/tools-iuc/tree/master/tools/fastp +name: fastp +owner: iuc +type: unrestricted diff --git a/sources/bin/tests/test-data/fastp_test/fastp.xml b/sources/bin/tests/test-data/fastp_test/fastp.xml new file mode 100644 index 000000000..dbf3c3fc6 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/fastp.xml @@ -0,0 +1,519 @@ + + - fast all-in-one preprocessing for FASTQ files + + macros.xml + + + + fastp + + fastp -v + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + +
+ + +
+
+ + + + +
+ +
+ + + +
+ +
+ + +
+
+ + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + + +
+ +
+ + + + +
+ +
+ +
+
+ +
+ + +
+ + + + + single_paired['single_paired_selector'] in ["single", "paired"] + + + single_paired['single_paired_selector'] == "paired" + + + single_paired['single_paired_selector'] == "paired_collection" + + + output_options['report_html'] is True + + + output_options['report_json'] is True + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
+ + + +
+ + + + + + +
+ + + +
+ + + + + + + + + + + + + + + +
+ + + +
+ + + + + + + + +
+ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 10.1101/274100 + + diff --git a/sources/bin/tests/test-data/fastp_test/macros.xml b/sources/bin/tests/test-data/fastp_test/macros.xml new file mode 100644 index 000000000..3e34427eb --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/macros.xml @@ -0,0 +1,58 @@ + + 0.23.2 + + + + fastp + + + + +
+ + + +
+
+ + +
+ + + +
+ + + +
+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/sources/bin/tests/test-data/fastp_test/test-data/R1.fq b/sources/bin/tests/test-data/fastp_test/test-data/R1.fq new file mode 100644 index 000000000..1209b20c7 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/R1.fq @@ -0,0 +1,8 @@ +@NS500713:64:HFKJJBGXY:1:11101:1675:1101 1:N:0:TATAGCCT+GACCCCCA +TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT ++ +6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE---;--..;.../9 +@M01368:8:000000000-A3GHV:1:1103:25519:6301/1 +AAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGCATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATTTCGT ++ +3A3AAFFFFBFFGGG2CF?4FGHGHHCHGGHHBHGFFAGGHHFFHHCGHFEGCECEGHFFFHGHHGFGHFGDAFDGFFEEFEGGBECC/;>=EF?AEFFFF;9;=DAFFFFBBFFFBFFF//;BFB.:FBFFBB/BFFFF/BFFE?EFAFEF9 +@M01368:8:000000000-A3GHV:1:1104:11928:24197/1 +ACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATA ++ +CDDCCFCFFFBCGGGGGGGGGGHHHGHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHGGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHGHHHHGHHGHHHHGGHGEEGGGGFHHFHHHGHGEHHHHHHHHHHHHHHHHHGGGGGGFGGGGGGGGFFGGGFGFGAEFEFGFEAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@D9 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+BBBBBFFBFFFFGGGGGGGGGGHHHGHHHGHHHHH6GHHHHFFGGGHHHHHHHHHHHHHHHGGFGGGEGGGHHHHHHHHHHGHE3FGGGGHHHHHFHHHHHHHHHHHHGGGGGHHFHFCGFHHGGGGGGGHHGGGGHHGGGGGGHHHHGGGADCHHHHGDGGGGGGGGC@DGFHEHHHHHHGHHHHGFGDEGFGFFGGGGCFGBEGFGGGFG;C.BFFFFFFFBFBFFFF/F?.AFFF/BFFEFFFFFEFF +@M01368:8:000000000-A3GHV:1:1104:7756:4776/1 +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +CCCCCCFFFFFFGGGGGGGEEFHHHHGHGHHHHHHGGHHHGGGGGGHHGHHHHHGHHGHHHGGFHHHHHHHHGHHHFHHGHHGFGGGGHHHHHHHHGHGHFFHFHHHHHHGGHGFGFHHHGHG?FGHHHHHHHHHHHHHHGHGHHGHGGCDGFFHHHHGHHHHHGHHHGFHGHFHGHGHGH/@CABFFFFFFFACAFF?BBFFBFD-@-.D>FFAF.F.:9---;AADFFFFFBEFFF:9FFFFBBFFFF/ +@M01368:8:000000000-A3GHV:1:1105:11310:21761/1 +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTT ++ +CCCCBFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHGHHHHHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHGHHHGHHHGHGHHGHHHHGGHGGG=FFGEHHHHHGHFGGHHGHHHHHFHHHHHHHGGHHHHHHHGHEHHGHHHHHGGGGF9AGE?DEGFFGGGGGGGGGGGGGGFFFF/9FFBFFFFFFFEFFFBFFFFFFFFFFFFEFFF0 +@M01368:8:000000000-A3GHV:1:1105:11578:14676/1 +ATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTC ++ +CDDDDFFFBFFCGGGGGGGGGGHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHFGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHHHHHHHHHGHHHHGGGGGGHGGHGHHHHHHH;CHHHHHHHHHHHHHHHGHGGGGFGGGFGGGGGGGGGGGGFGGGEGGFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1105:13575:19255/1 +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGTTCCCGTGAGTGGTTAATAGGGTGATAGGCCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG ++ +AA1A1DFFFFFBGG3A111FFAEGDDBGFDHF00F01BBA00BFGEHFBFFA1FABB0FAE?CFHF1BGFHFB0011F121E//>>1F10>B?EFHGCC/?/BFG/EEGFFEE//BCFDE0?E@@B/?11AAFFFFFEAGGGFGGAA6FHDGGCGFHFFHFHFHHHHHGDDDFFFHGFFHGBEGEGHHHFFFHGEEAEGHHHHHFHHHFHGHFEDGGEGBEAGEFHHFFHHHHHHGGHHHGHHGBGHHFHHFGHHHHG?CG?AFHH1FHHHGHFHHHF?DGHFFHCGAGEFHGCBBBB?BFFF?B-B.9/BFFFFFB=-AD?..@FFFF@@-@@?AFD.FFFBBEEBD9/:FFFFFBB/:FF9BF/BF.BBFF/: +@M01368:8:000000000-A3GHV:1:1105:21099:2895/1 +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTT ++ +CBCBBFFFFFFFGGGGGGGGGGGGGFHHHHFHGHHHHHHFHHHHFGFHHHHHHGHHHHHHGHHEHGGGGHHHHHHHHHHHHHHHHHHHHHHGGHGGHHHHHHHHFHHHHGHGHHHGGHHHHHGGHFFGHGCGGGHGHHGHHHFGHHFHH/FGGGHFGFEGGCFCCD;B@DFFFFFFFFFFFFFFFFFFFFFFFFF;F.BEFADFFFF.AEFFFFFFE;D.;:B00099:09BFBFFBFF.0:000BFFBF0 +@M01368:8:000000000-A3GHV:1:1105:26469:19245/1 +TTATGATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCAAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG ++ +BAAAAFFFBFFFGGGGGGFFGGHHHHHHHHHHHHGGHHGHHHGGHHHHHHHHHHHDEGGHGHHHHHGEDHFHGFHGGHHGGHGGEHHHGHHGHHGHHHGGEGGGHGHGHHHHHHGHHHHGHGGGGGHFHGGGGHHGGGGCDGHHHGD>A@FFFFFFFGGGFEECFGGFFB5GBHH5DFH5GBEEAEFHFHHF3F3GHFHHHEF3GAEHBGFHFFEFFHHHHFFB31FGGEGFHGEHHHHHHHHHHHHHHHHHEEEEGHHHFFF3GF3FGF44BBGEHHHHGG2B/BGGHE;B=.9.;.BBFFF..;A;/B/;B//;;//BBF/ +@M01368:8:000000000-A3GHV:1:1106:22927:3863/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGACTTCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAA ++ +A>ABAFA?D@AFGGGGFGGGFGFHHHFFH4BCBGHHHHGFFF3G5BF3322EEAFHHHHHHAB5GHFHEHFHHH3BEEHFGF5@13FDF3GDGFHHFGHHHGHHHGFGGHHFCG//?/EGHHHG3F4BFFGHHHEDGFHHB/B/?FBF<@-9?BDEFFF?B--?DFFFB9FA>B;A.BFDB?AB.--@;-.FFAEFFFF9AE;DDFFFFB/9BFFFFFFFB:BF/BB/BFF//FFF-=--.99=--.9/// +@M01368:8:000000000-A3GHV:1:1106:23625:4236/1 +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTA ++ +@?AAAFFBFBFFFGGFGFGGGEFCGGHHHHFGHGHFHGHHHHGGFGGFGHHGHGHHHHGHGFFHHGGGGGHHHHHHHHHBFHHEFHHHHHHGF?FAGHGFHHHGDGFHHGGGHGHFHHHGHHHGHHFHHGFFGFHHHGHHHHFFHHHHH/FGHHHHGHGHGDFFFE?FFF/--;;9/:BFFFBA///9----;B.//////;...---9--- +@M01368:8:000000000-A3GHV:1:1106:6455:17124/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBAAFABDBBFGGGGGGGGGGHHHGHHGHHHHHHHHHGHHGHHGHHHGHGGGEGHHHHHHHHHHHHHGHHHGHHHGGHGGHHHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHGGCFEHHHGFHHHHGHHFFH?GGHHHHGHGHGHHCFGGGGGGGFFFFFFFFFFFFFFFFFFFFADFA?.FEFAFFFEFFFFFFFFFFFFDABFBBFFFFFFFFEFFBFFFFFFFFFFF/FFBFFFFFFADE>BFFF9 +@M01368:8:000000000-A3GHV:1:1107:14451:26748/1 +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BABBBFFDABBBGGGGGGGGGGHGHHHHGAGHGGGGGHHHHHHHHGHHHHHGGGGGGFFHHHHHHHHHFHHHHHGGGGCHFHH3FEHHGCGGGDGHHHGFGGHHGGGGHHHHHHG/DGGGHHHHGGGGGCCHGG?CGG1GHHGHHHHBGHHHFHHGHHHHGGADAD00ECEGHEFHHFFAEFFFFFGGFBFBFFFGFFG.;B/99;BCFGGGGEFFFFFFEDA./:ADEB?FBFFFF;FFEBFBFFB./9. +@M01368:8:000000000-A3GHV:1:1107:18714:24788/1 +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BBBCCFFFDEDEGGGGGGGGGGHHHHHHGGHHGGHGGHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHCFGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHGHHHHHHHHHHHGHHHHGGEGEGCCEGGHHHHHHG:CAFFGGGGGGBFEFGGGGHGAFFGGFGGGGGGGEFFFFFFFFFEF/EDDFFFFFFFFFBFFFFFBBFFBBF/ +@M01368:8:000000000-A3GHV:1:1107:21355:8333/1 +ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +ABCBBFFFFFAFGGGGGGGGGGHHHHHHHHFHHHHHGGGGGHHHHHHFHHHGHHHHHHHGGGGGHHHHFFGHGHGGGGGGGHGGEGGGHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHGHHHFHHHHHHHHGHFFHHHHGGHGEGHHGHGFHHFHGHCEFHEGHGHHHGHHHGGGGGGCFFFFBFGGFGGGGFBG?FDGGGEGFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF.AA/9 +@M01368:8:000000000-A3GHV:1:1107:22864:15712/1 +AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATG ++ +BBBBBFBBFFFFGGGGCEGGGGHGHHDGFHHHHHHHHHHHHHCHHGHFGBGDFGE?GHHGHFBHHFHHHHHHHHHGHFGFGHGHHGGC@DCFGHHGGGGGGGHHHHHHGGGGGFGGGGFFGGGGFADGFEFFFFFFFFFFF9;FFFF/BFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFEAECDFFFFFFFFFBFFFFFFFFFFFFFFEFBFBFFF/FFFDF-;-9;E@>-9DFFF/FFBF;-.:;.9A// +@M01368:8:000000000-A3GHV:1:1107:24817:14233/1 +CTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACAT ++ +3AABABFFBFFFGCFGGGGGGGHHHFGCFGGGFFGHHCGHHHGHGHGHBFFHHHEDGGFGFGHHFFFHGGEGHFHHGHFHGFFHHHFGHHHFHACECEHHHBGFHGFHHHFHHF4GFHFHFHEHGGE/EG:A-CFGGFGADGGGGFGGGGDAAAADFA.-AFFECFDAAFFFFEFFFFBFF;D;BFFFB/;BFFFFFFFFFFFFFFBFFBF/;//;BFFFF?FFFFFFEDAFFFFFBF//:BFBACF--9/ +@M01368:8:000000000-A3GHV:1:1107:24830:14440/1 +AACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +ABBBA@FFFFBBGGGGGGGGGGHGHHGHHGHHHGGHHHHHGHGHHGDHHHHHHAGGGGFHHGHHHHHHGHHHHHHHHHHHEGAFGFHFHHHHGEGHHHHHHHHHHHHHHHHHGGHHHGEFEGGHHGHHHHHGGHGFHH/?GHHHHGFGHGFHCGGBBDAFFFEFFFFFFFFFFFFFF=CDDADDFFFFEF=BFFFEFFFBFFFFEEBF./:FFFFFFFFFFFFFFFFFFFEFFFFFFFFFFF/BFBEFFC- +@M01368:8:000000000-A3GHV:1:1107:26478:23602/1 +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACCTCTC ++ +1AAAAF1B13BBBEGGGFGGGGGGHHDB1BGFHHHFGFGGG0F00BGBGFGGF1GBGB1BGCGAEE/FGFHGHFHHHHHBFF1B0FGGF//F//FGFGFFF/1@B1DFHHHGGEFEDHFDFAFF0B//1FDD1GFFHHDF?1BD>GF/GCAC0C@?@-;99BBB->@--;-B//99B--9-BF=A--A-:A----9AA9AFBFBBB?E@BBFFFFFFFBFFFFFBFFFBBFFF//B/////-;9 +@M01368:8:000000000-A3GHV:1:1108:11059:23181/1 +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGAT ++ +CCCCCFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGHIIIHHHHHHHGHHHHGHHHGGHGGHHHHHHHHHHHHHHGGGGGHHGHHHHHHHHHHHHHHHGGGGGHHHHHFGHHHGGGGGGHHHGGGGGHGGGGHHHHHHGGGGGGHGGHEFGGGGGHGGG-ECHHHGGGGGGGGGFGFFGGGGFGGGCF?EFGG0;BFFFFB?9AAFFFFFFBF;BBFFBFFFFE?F/ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/1 +TAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCCTGTCTCTTATACAC ++ +BCCBAFFBCCCCGGGGGGGGGGHHHHGGGGGHHHHHHGHGHBGFHHHHHGGGGGHHGGBFGHHGGGGGGGHHHGGGGHHGGGFHHHHHHGGGGGGHGHHGGGGGGGGGGGGGGHHHHFHHHGHGHHHHHHGHGHHGGFGGGDFFGGHHHGHGH/FHHHFHGHGHHGHHHGHHBAAAA3BDFFFFDGBFFEEGGGGHHGHFHHCFHGHGHHHGF3BFGFHGFEFHFHGH3EGFC1EEGBFGBHFGGFFHHHGHFHGHHGHGGHCEHEBCFF3ED3@GH4FDEG12FFHFFHG/G3FGA/@EFEFCG33FFGBBGHFHH/?BFBGFGFAGC2C/@-;@-;BFFEFADF?DFFFFFF?;AFFA;AD;..FEFFA--;9;D.9BFFBE?;.;///://///99//BB/9;F./B//BBFB9////99/ +@M01368:8:000000000-A3GHV:1:1109:25237:11722/1 +CCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATATCGTATGCCGT ++ +AABBBFFFFFBBF5BGGFGABGHGGAEFGFHHHHFHCHFHHBFGGGEHBGGHFFFFGFAEF5FHH?EGGF5AEG3?EBFHD?C/EFHFFEGEE?CFGGGHHFHB3EEFG?EEGHCFGGGGGGGECA?FFFDFBFGCG4EGFG??GACFGGHFHCFHCHBECDEFCEGHHHHHFFGGF3AFFHHFGEGCGHHGEHGFGHHEGG?EFHHH?EGGHHGGGGHHHHHHEGGGGGHFHHGFDDGGACFCC@?/FDDGHHHGHEFFHHH0FDHHFFEDCD.CFHHGDFGGGGGEFGC?EGHHHB0CGHHGCGHHHHBEHGHH.::ACA;FECFGGGGGFFFEFGGGGGGGFFBBBFGBFFFEFFFFBFFFFFFBBFBFFB9..AF?FFFFFFF9 +@M01368:8:000000000-A3GHV:1:1110:14751:26540/1 +TAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACTGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGTTGTGCACGCGATAGCATTGCGCGACGCTGGCGCCGGCGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG ++ +AAA?1CFFFFADGEEGFGB1112DGDGHGFGHHCG/ECEBGGHDFGHHFHGHEB1BCGFFE2EGHHGHFFFHHBFFHEFCGGHHFHHHHH111BFFHGHEHBEHGGECEFHGFHFGGDBBGHHBHHHH0GH22FGHGFFFH1BFCG0F@FGG11@GDHFG1D/1FGFHH/FCG.>0><-<@CCFFG.CC-@C?C9FFF0C---;------;9----9-9@-AAFF9B9---9-/;B9BF/9BB//B/;/// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +BBBBBFFFFFFFGGGGGGCBGGE?GGGHHHHHGHHBEGGHHGGGGGHHHHHHHHHHHGGHHHHGFGGGGHGHGCFGHHHGGGCGGHGHGGGGGHFGGGHHHHHHGCEFGGHHHHGGGGGGGHGG/CEGHHHHGFHHHGFHHGFFHGHGHFGGEGFDDGGBCGHHGFHH/CHHHHGHGHF0CFGGGGGGGFFFFFBFFFFFFGFFGGF?DGEDEEFEFFFF?FFFFFFFFFFFFFFFBFFF.BFFFBFBBA; +@M01368:8:000000000-A3GHV:1:1110:16559:7507/1 +CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAACTGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +ABBBAFFFFFFFFGGGGGGGFGGGGAGHHGCHHGHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHFGGGHHHHHHHHBDHHHHHGGHFEEGHGGHHHHHHHGHHHEHFGGGGGGHHHF33FGHHG3GDDGH//EEGHHFFBF?GHHFCC@DGFCGGB?DGHAFGGHHGFH0E??<@DGHGGCFGGF?DGGGFFGGGGGGGG.C/0BBF?FBBEGG0FFF.AA9;B9/E////99;;:.//:FFFFBBF//9 +@M01368:8:000000000-A3GHV:1:1110:16700:6843/1 +AAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCTGTCTCTTATACACATCTCCGAGCC ++ +BBBBBFFFFFFFGGGGGGGGGGHHHHGHHHHHHHHHHHHGGGGGHHHHHGGHGHGGGGGGHHHGFFGHHGGGGHHHHHHCGG@FGHFHFEGGGGGGHGGGGDGHHHHHHHHHHHHHHGHHGHGHHGGGGGCGHEHGHHHFHHHFF.DGHHHHHHGHHHHHHGFGHGCGHGHHHHHHHHGHHHCD?:A::FCDGEGFGFFBFGBFGGGF00CBFFFF/BFBFFFFAE.FBBFBFFFFB/BFFBFFF/ADCAD +@M01368:8:000000000-A3GHV:1:1110:18014:7856/1 +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTTCTGCTTGCAAAAAAAAAATAG ++ +AABBBFFFFFFFCGGGCGGGGGGHHHHHGFHHHHHHGHHHGGGGGFHHGHFGGHHHGGFGGGHHGGGGGHHGGGGHGGHHHGGGGGGHHGHGDGGGGGGGGB/A99FE//BBFFF.9/FF?DA=@9./9 +@M01368:8:000000000-A3GHV:1:1110:23303:11846/1 +ACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTC ++ +3ABB?FAB?DAAGGGFBGGBB5AFFFGFHHGGGEGHHHFHHF3EGFHHHHEFHHGGHHHGH3EFHHHHHBDGHHE?ECHGHGHHHHHHFHHHGHHHHHHHGGHGGFHHHFHHGFFHHFEGFHHHHHHEHHFDAGHHHH/BDDFGGH1FDBGHHHHHHHCGHHHFH?0CGCF>CC=@--AFBFFB?=BFDFFF//FDB;-9A-AD-.A.A=?-9-:B/AEB/BFF.A;DDFFFBBFFFF/BBFFFFBFF9B; +@M01368:8:000000000-A3GHV:1:1111:13195:14562/1 +ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTCCGAGCCCACGAGA ++ +ABAAAFFFFFFFGGGGGGGGGGGHHGG4FDFGFGGCGGGHGHG?EGHEGFFDHFHHHHGGFE@EHHGEEEGFCCEFFGFG/EHHHHHBFBGGHFHFHEHGHEFGGGED/EFDEFFEHHBGHHCFFFDFGGHHGFFFHHHHGFG>0<0DGGFHBGHFBDFGHGFFGGAGHHGCGBHFFHHHFFFBFGGGGF/:FFFCB9F9FF0FEFE?FF0BED-D.//BF9//BBFF/BFFFEFFFFED-DCFF?.:BFA +@M01368:8:000000000-A3GHV:1:1111:14287:20817/1 +GCCAACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTCATCGCACCTACGTTCACTATTACAGGCGAACATACTTATTAAAGTGTGTTAATTAAT ++ +>>A3>AAAACFFFGFGFGGGGGHGHHHHHHHGGGGGHGHFFCGHHGBGHFHHHHAGHHHHEHHAGFFEHEAE?GHHHHEGFFFDGHGHBFFHFHHHGHGHGHBECG@@@EHGGEGCGGGGFFGGGG?BGGGGGG.-C.FEDCFFFEFFFAF/99BEFA.:9BFB/9FFFEFFFFFFEFFF/FBBFFFFFFFFFFFB//;.@@//;DFFFF//BBFFFBF;A;DF=>B//;9B//B/;/;9//9//;B/:B9 +@M01368:8:000000000-A3GHV:1:1111:23624:14516/1 +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGGGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAG ++ +3>3AAFFFFFAFGGGGGGGGBGHHHHHHGGHGGHEHGHADFHHHHEGGGHBGHFFHHEHHGHFHGG5FBEEGEGHHHGHHHEFDGHHFFGFGGHHGHHHGHBHGHFHFHHGGGGFCFBGFGE?GFBECEGDGHEHGDGCGHGC/DF@GHGFFCGGGGFFFFDD?@C@GFEC?-ADHFFHBGHFBHFG0CC//.;B0/CA.;AA.;@.AB/9BB/A/.AFFFE/BFFF///9B/FBDE9/;99/B/BFFEF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/1 +ACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTGTCTCTTATACACATCTCCGAGCCCACGAG ++ +CBCCDCFFFFFFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGFFEHGGHHHHHHHHHHHGHHGGGGGHHHHHHFHHHHGHHHHGHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGCGHHHHGHHGHHHHHHHEDHHGHGGGGGD;BEGGGFFGGGGC:CFGGGGGGGGGFGGGFFFGFFFFF;FFF;BFFFFFFFFFFFB:FFFFD=CAEEEF>- +@M01368:8:000000000-A3GHV:1:1111:8665:25542/1 +TCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTGTCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +AA3AAFFFFFFFGGGFGFFGGGGHGH4AGGGFHHCGEE2FGHHHHHHHHHHGFHGF53FHEGGFAF5CFHHGGFGHFHHGGHHHCHHHHHHHFHHGH?EEEG1FFFEHHFHFGGHHGG?F4FBGHGHCHEF0//-9--;0CFGG?@BGDGFFFFEFBBBDA?FFBFFFF=B;-9.AA9EFFFF/;9BD.//;9/9/B:/:BFBFFBFFF/B:BFF//;/B/FFFBFF.A-BFFFBA/F//BFFFBF/;/A- +@M01368:8:000000000-A3GHV:1:1111:9655:13916/1 +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +1>>1AAFFFFFBGGFE1EEEEGGHGHHH2FGHHHFGFGHGCFGGGEFHGGEGGHHHHGHEFBFEGHHHGHHBEHHHHGHGFHHHGGGGHHEGGGGHHHGFHGHHHH1FHHG?G/AGF1GBFGEFFHF2FDD0FG--99@=---AAABA-BF/B?A@F-9BBFF//BB/9/ +@M01368:8:000000000-A3GHV:1:1112:10272:7828/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCTGTCTCTTATACACATCTCCGAGCCCACGAGACTAAGGCGAATCTCGTATGCCGTCTT ++ +AAABABBBBBBFGGGGGGGGGGHGHHGHGHHHHHHHHHGHHHGGHDGHHHGGGGHHHHHHHHHHHHHHHFHGHHHHGGHGGHHHFHHHHHCGHFFHHHHHHHHHHHHHGHGEFGAEEEEHHGHHGHGHHHHHHHGHHHHHHGHGHFFBC/BA?BGGGFFFFFFFFFFFFFFFC-@DDFFFFFFFEFAFFFFFFBFBFFFFFFFFFFFFFFFFBFF->@FFFFFFFFFFBFBFAD--.99;A?////:.9A. +@M01368:8:000000000-A3GHV:1:1112:9832:16531/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC ++ +AABABFFFFFFFF4GGGGEBGEFGHGGHGHGHHHGGHFBGFGGGGGHHEFHGEHFHFHEHHHHHGCGGGHFHHCFGHE@1EEEFFGB?EEEEHBGGGCHHGHHBEE@>EAHHFAEBDGGGCEFF?CEGFFHHHHHFHHHFHGHCGCAHHF<..C.D=0CD.GFHHHG.CAGHC:CHB0GGGFFB0:CFA.A-;9.;000CBBFFBFGA.9AA;A;EDDE.ABBFFFF9;BEFFF/BF//9/B//9:B//.. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/1 +CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA ++ +AABBBBFFFFFFGGGFGGGGGGHHHGGHGGHHHHHHHHHHHGHHGGGGGHHHHHHHHHHHHHHHHHHGGCGDHHHHFGGHHHGGGGGFGGHGGGGHHGGGGHHHHHHGGGGGGHHGGGGDGGFGHGGFCDCHHHHGHHHHGHHFAGFGGEHFGEG.C1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF +@M01368:8:000000000-A3GHV:1:1113:5741:16959/1 +TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA ++ +ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9;BF9FF9FFFFFFFFFFFFFF?BB?;9EE;-;DDB9//;B-B@;ABFFEFFFF/-.9A.;//9/BF./B/..9.9:...////// +@M01368:8:000000000-A3GHV:1:1114:14540:5315/1 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT ++ +AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/1 +TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA ++ +BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/; +@M01368:8:000000000-A3GHV:1:1114:2404:13066/1 +TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCTGTCTATTATACACATC ++ +CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFFFFFFFFFFFFFFFFEFF0 diff --git a/sources/bin/tests/test-data/fastp_test/test-data/bwa-mem-fastq2.fq b/sources/bin/tests/test-data/fastp_test/test-data/bwa-mem-fastq2.fq new file mode 100644 index 000000000..ff3c56bb5 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/bwa-mem-fastq2.fq @@ -0,0 +1,400 @@ +@M01368:8:000000000-A3GHV:1:1101:6911:8255/2 +TCGCCTTACCGCTACTCACCCACGGCGGCCATCAGCCGATACTAAGTTTGGGGTATGGTGGGGGGGATAATGAATTAGGTTGTGGGGGAGGGTTTGTGGTTGAGAGAAACACAAAAAACAATCTTATATATGGGTAGTCGTTTTGTATTGGTTTTTTGTTTTGTTTGTGTTTTGAGTGTCGGTTTAGTTCGGTGTACTAGGGGGGGTGGATGGGGTCGGCTGGTGAGGGGGTCTTAGTGTATTGAGTGTGG ++ +1>11111@11111A111A100000000////011110//>>/12@1@22B/////1@>21/>>/-----9/;////9////--;-;-;-----;--------9/-/-///9-;-------9//////9/////-//-/9-;-;9--/////99-;--9-:-;----/---/-----////---9-/////--;A-//////---------9/-----;-----/-/-----;--;//////////9;///- +@M01368:8:000000000-A3GHV:1:1101:14518:9998/2 +CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA ++ +CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0 +@M01368:8:000000000-A3GHV:1:1101:18422:19051/2 +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF +@M01368:8:000000000-A3GHV:1:1101:25545:21098/2 +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT ++ +3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<.<<AABBFFCFFFGGGFGGGGGGGGHHHHHHHHHHHHHHHHHHGHHHGGEGGFFHHHHHHGHGHGHHHHHEHFHGHHHHEFHHGHGGGGGHHHHGHHHHHHHHHGFGHHHHHGHGHGHHGGGCCGGGGFGGGGGGDGGGGFGDGGGFFFFFFEFFFFFFFBAF:9AF//;BEF-DD/FFFFBFFFFFFFFFEBFF?FB;/;//BFFEFFE/::..9;-:B9:FBFFFFFFBFB/9/FFF/B///99/:B/// +@M01368:8:000000000-A3GHV:1:1102:17584:10050/2 +GTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGATCTTGGGGGGTGG ++ +ABCCCFFFFFCFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHFHGGHGGHHHHHHHHHHHHHHGHHHGGHHHHHHHGGHHHHGGGGGHHHHHHHHHHHHHHGGHHHHHHGHGHGGHGGFGGGGGGGGGGFGGFGGGGGGGGGFFFFFFFFFFEFFCFAAFEFEFFFFFFFCFDFFFFFFEFFFFFFFFFFBFFFFFFF/:BFFFFFFFFFFFFFFFFAFC=@-.;A///B././//////.-9---- +@M01368:8:000000000-A3GHV:1:1102:18842:24844/2 +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +CCCCBFFBFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHFHHHHHGHGHHHGGHGGHHHHGHHHHHHGHHGGGGGHFHHHFGHHHHHHHHHHHGGGGGHHHGFECGGHGGGGGGHHHGGGGHHGGGGHHHHHEFDCADGHHHHGGGGFC?AE-@DDFHFFHHHCFHGGFFGFFFGGGEFEGFGED9C?CEGF90FEF/A./BBF9FFFFFFFFBFFF.9AF////;FFBFFB/:BF +@M01368:8:000000000-A3GHV:1:1102:21788:11027/2 +AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCCTG ++ +CDDDDFFFFDDFGGGGGGGGGGHHHHHGGGGHHHHHHHHGHHHHHHHGGHHGEHGGHHHHHHHHHHHHHHGGGGEHHHHHHHHHHFFFFFHHHGGGGGHFHGBFEHHHGGGGGGGHHGGGGHGGGGGHHFHHHGGG@CGHHHGGGGGGGGGGGEGDGFFDHHGEHHBCFHGBGFAGGHFGGCEEF0BE///FDFACF?FHFGC//??1B0<FF>DFCFDFFFFFFFFF-BBAFFFFFFFFE@D9B;FBFFFFFFFFB9/9FFFEBF9/B/BB/BFAADDFFC-;;9-;@@9-.9/://///://///...- +@M01368:8:000000000-A3GHV:1:1103:25465:20010/2 +AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCACCCTATGTCCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGGTCTTGGTGGTCGTCCTCGTATTTGAACACATAATCGTG ++ +AAABBFFFFFDFGGGGGGGGGGHHHHHHGHHHGFHHHHHHHGGGGGHHHHHGHHHHHHHHEHHHHHGHGGHHGGGHHHHGGGGGHHHHHEHFGEHHHEE14BGHHHGHGHFCE/EFGGGGGGHGGGGGG?FFGGGG.ADGGGFFDA.FFEC--;9BBBD?FFFFFFFFBBFFFFFFFFFFFFFFFFFADFDFFC-BBB;BF-.;9:B9B9/9/;9;//;:.99/;-...:.../;//////.9/////.;. +@M01368:8:000000000-A3GHV:1:1103:25519:6301/2 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATGCTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGATGTCTTATTTCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGAT ++ +>AABBFFFFFFFFFFGGGCAFGCGHGGGHGGGHHFHHHFHHGGGGGFFFHHHBHHHHG5BG5GFEEEE1FGFFGF1EGHGGG/BFHEF@EA1BE1@EED3?4DHGGGGEGHFFFDDG?DCDEG@<?@DGCAGC-;@DGFFHGCHEEFGGFGFB/;..BBB.CCE?A0FE0EBFF0FEF.;=DFFB//BFBF//;/:9BA.9FB9//;9//;9F;FF +@M01368:8:000000000-A3GHV:1:1104:13832:4398/2 +GACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGTAGATCTCGGGGGGTGCCGGCTCATTAAAAAAAGAAGATGTCGAGATGTCAGTGCGTGAGTGGAAGTG ++ +BBCCCFFFFFFFGGGGGGGGGGGGGHGGGGGGGHHHGFGGHHFGGGHGHHGHGFGECGHHHHGGGGGGGHEGFGGGHHGHFHHHHFGHFHHHHGHHHHFGGFGG3FFGGHHHHHHH2?FFGHFHHHHHHHHHBGHDGC0FGHHGHHGHHHHHHHHHHFGHHGGGGGHG-:@?FAGA:.:09CB0000;9B0.9-;---:./----.0;B00;:0;;.../90009..-..00000000-...90:.00/00 +@M01368:8:000000000-A3GHV:1:1104:23670:4161/2 +CGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAA ++ 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+CCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAG ++ +CCCCCFFFFFFFGGGGGGGGGGGGHHHHHHHHFHHHHHHHHHHHHHHGGHHGHHHHHGGGGFHHHHHFHHHHHHHHHGGHHHHHCGGHGHHGGGGGGGHHGGGGGGGGHHHGHHGGGGGGGGGGGGGGGG@CDE?EFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFE;DFBFFFFFFFFFFFFFFFFFFFAFFFFFFFBFFE0BBBFFFFFFFFFFBFFFF9BB0:0:B; +@M01368:8:000000000-A3GHV:1:1108:7626:10048/2 +AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGATCTCTGGGGTCGGCGGATTT ++ +BCCDDFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHFGHHHHHHHHHHHHGHHHHGGFHHHFGGGGHHHGHHHHHHHHHHHFGHHHHHGHGHGHHGCGCGGFHHHGGGGGGGGGGGGGGGGGGGFFFAFFFFFFAA-AFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBBFFDFFFFFB-<>;>@BE<:000.0.0/0<00<0:>..-<<<---.0 +@M01368:8:000000000-A3GHV:1:1109:11270:12255/2 +CTACCTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGATT ++ +BCCCCFFFFFFFGGGGGGGGGGHHHHHFHHHHGGGGHHHHHHHHHHHHHHHHHHHHGHGGHGGHHGHHHHHGHHHHHHHHHFHHHHHGHHGHHHHHGGGGGHHHHHHHHGHHHHHH?FHHHHHGHGHGHHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFECADFFFF.DEBFFFFFF;D.B;.ED.FFFFFFF-.:00009BBF +@M01368:8:000000000-A3GHV:1:1109:24217:19077/2 +TAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGAACCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTTCTGTC ++ +BBBBBFFFFFFFGFEGGCFGFGHHHHFHHFHHHHHHGGEEEFGHGFFAGFFEEAEGGHHBEEFAFGAEF1G3GFGGEEF@EAGGHGFF?ECGGHEEEFGGHHHHFHHFHHGFHHHC2DAGHGG00-BFFA9FFFFFFFFFFFBFAFFAFFFFFBFFFFFFF/9BFFDFFDDFF-9@CDAD;:AFF/;B//....;;///; +@M01368:8:000000000-A3GHV:1:1109:27103:7153/2 +NTACTTCAGGGTCNTAAAACCTNAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCANGGNAGCTCTCCNNGNNNNTGGTATTNTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACCTGTCTC ++ +#>>AAAFFFFFFG#AAFFGGGG#BAFFAGHHHGGGGHGHHHHFHHHHHHHGHHHHHHHEGFGGHHBGHGHHBGFFEG2GHHFHFHHHGHHGHFH#/B#??FFGHHH##?####????FHG#??CFGGGEF>CGAGAGGGFGAA@@FFFFFFFFB=@@FF?FF;FFFF@@-@-AFEF?BB/BF?E-BBFFF;:BB/BFFFB/BFFFBFBFBBFFFFFB/FFFBB/;9A@@BFFBFFFF/BBFFFFFFE/:9/ +@M01368:8:000000000-A3GHV:1:1109:8763:7859/2 +GGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG ++ +>AAABFFFFFFFGGGGGGGGGGHHHHHHHCHFAFHHDGEGFHHHHHHHHFHHHHFHHHHHHGHGGHGGHHHFHGHHHHHFFHHHHHHBGHFFHGHGHHHHHGGEGGHHHHHGHHHHHHHHHGFGHHHHGHGHGHHCCGGGGGGGGGGAAGF?FFFFBFA@=BDDFF?-;FFF;@CFFEFEFFFFFFFFFBFDFFFFFFFFFFFFFFFFFFFFFF:FFFF/BF/FFFEFF?DECAFEFFFFFE:FFFFFFFB +@M01368:8:000000000-A3GHV:1:1110:12808:18367/2 +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACAGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTCTT ++ +ABCCCCDDDFFFGGGGGGGGGGHHHHHHHHHGGGGGGHHHHFHHGHHHHHHHHHHHHHGHHHGGHHHH3GFHEFHHHHHGHHGFHHHHHFGHHHHHGHGHGGHGGGGGGGHHHGGCGGGGHHGGGGGGGGGGGGGGGGGGGF-BAEFEBEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFAFEFDFFFFFFFFFF0BFBED=@DFFFFFFFFFEFFFFFBFAFB;0:;F0 +@M01368:8:000000000-A3GHV:1:1110:14751:26540/2 +ATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGGTTGGGCTATTTGGGTTTTTTGACCCTGAAG ++ +BBBBBFBBBBBFGGGGGGGGGGHHHHGGFHGGHGGCHHHHHHGHHHGHHGEGGGHHHHHHHHHHEFHHHHHHGEE?FGHGEHGGHHHGGGGGGEHHGGGGHHGGGEGHHHGHGGGDFGHHGHGGGGGCGAFFCCDFHHHH1CGGHBHFHFCGFFCDFHGCCE.CC:EGFHHCGHHGCF?FGGGFGGG;B9;FFFFFFEGEBF0;;;0;CFBFFF?D.DE.:..99-...;;//9A.;DE.9-./:FB.;// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/2 +GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG ++ +BBCBCFFFFFFFGGGGGGGGGGHHHGHHHFHHBGHHHGGGGHHHHHHGHHHHHHHHHHHHHHHGGHGGHHGHHHGGBGHHHHHHHHHHHHHHHHHGGFHHHGGGEGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGDGGGGGGGGGBFFFFFFFFFFFFFFFFFFFECB-=BFFFFFFFFBB?E-A::FFBFFFFFBFFFFFFFFFFFFBFFEFFF;0BFF0:FE?FFFFBFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1110:16559:7507/2 +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAAT ++ +>AABBCCCCFFFGGGGGGGGGGHHHHHHHHHGGHGGHGHFHHHHFHHHHHHHHHHFHHGHHHHGHHHHHGGEEGHHHHHHHHHHHHHHHHHHHHHHGHGHGHHGGGGGGGHHGGGFGAGFGGGGGGGGGGGDDDFAGGFFFFCFAFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFE..@BFFBD./;:0FFFFF09B/AFCA=-99BFFBFFFFFFFB:BFBFFBFB9: +@M01368:8:000000000-A3GHV:1:1110:16700:6843/2 +GTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTCTGTCTCTTATACACATTTGTCGCTC ++ +CBCCDFFFFFFFGGGGGGGGGGHHGHHHGGHFHHHGGGGGHHHHHHHHHHGHHHHHHHHHHHGGHGGHHHHHHHGBGFFHHHHHHGHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHFHHHHGHCG/GGHHGGGGGGAFGEEADAGGDFFFF00D>CFDDFFFB?AF?B;-@>.FEDFFFFF0BF-BDFFFFE00B0BF0FFFF:BFA0B0:BBFBBFFFFF0B0:000<00FDFFFFFFFFFFFBFFFFFFFFFFF/FFF/BFFFFFFFBA.?@;FFBDFFFF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/2 +ACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTCTGTCTCTTATACACATCTGACGCTGCCGAGA ++ +BBBBBFFBABBBGGGGGGGGFGHHHHHHHHHHHHHGHHHGFHHHHGGGGDHHHHHHHHGFHHHHHGHHHHHHGHFHGHHGGGDFGDFFGGGFFGFFGHGHHHGGC?AD-:A-AFFGGG-?9EFEFGGFFBFEFCFFFFFFFBBBFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFEFFFFFFBFFFFEFEFFFF;CF-FFFFFFFF/BFFFFFFFFFFFFEFBFFFB/FFFFFFF//9A..;F--@9 +@M01368:8:000000000-A3GHV:1:1111:8665:25542/2 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGACAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTA ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHCHHGDGGGGHGGHHHHHHHHGHGHHHGGGGGHFHHHHFHHHFFHHHHHFGCGGEHFHHFGGHFHGGGGGGHHFEEEAFEFFDFHGHHHHGGGGGGGHH0DGGGGCGHCC-FFFFFFFGGGGGGGGGGHHHHHGHHHHGHHGGHHGGHGGHHHGHHHHFHHGHHAFGGGHHHHHGHHHHFHFHHHHHECGGGHGHHHEFHFHGGGGGGGGFGFFGFFEFGEGHHHGHHGGDGGGHGFGGGGGGGGE@GCGGHHHGHHHHHGHHHHFHHGEGFFEGCE.ECCECEHCGGFFE/AABFFG0CFE0BFFF9CFGG.F/BBBFFGFGGGFFFFFFBFEDAEFFFFFBFFFFFFF0;FEBF: +@M01368:8:000000000-A3GHV:1:1112:10272:7828/2 +GTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCAAGTGTAGTGCTCGGGGGGG ++ +BBCCBFFCCCCCGGGGGGGGGGGGGGHHHHHHGGGGGGHHFHGGGGGFGHGGGGGGHHHHHHHHHHFHHHHFHGFFHHGF?ECEFFFFFFHHHHHH?FHHHHHHHHHGFHHHHHHGGGFGHHHHFHHHHHHHHHHGGGFGFGCGGGGHHHHHHHHHHHGGFFHGHHHHHFFHFCGFHCCGHGHCGGHG?DGGGGGFBBFGFBFBBBGGGB0000;CD?DFFAFF9=--;...://;////////.------ +@M01368:8:000000000-A3GHV:1:1112:9832:16531/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBBFBBBBBFGGGGGGGGGGHFHHHHHHHHHHHHHHGHHHHGHFHHHGEEGGHHHGHHHHHHHHHHHHEHGHHGGGHGGHGHHHHHGHHHHGHHHHHHHHHHHHHHGHHHHHGEGCGHHHHHGHHHHHHHHHHHHHHGHFFGHGHHGGGDACDFFFFABFFFFFFFFFFD-BC?DA9.DFFBEA==B=?F.;ABBFBFEF-DAF/BFF9/FFFBB/9BFFFFFFF/BFBBFFFFFFF/9FEA?--B/;. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/2 +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATT ++ +BBBBAFFFFFFFGGGGGGGGGGFGHHHHHGHHHHHHHHHHHHCGHHHHHHHGHHHHHHDGHHGGAECHHGHHHHHHHGHHHGHGFHHHHGGHGGHHFHHHHHHFHHHHHHHHH2GHHHHGHGHHFHHGGFGGGHHGHHHHHFHHHHEFHHHHEFGFFHGEHCFGDFDFFFFFCFFFFFFFFFFFFFAFBFFDFFFFFFFFADCF?9?EFBFB9EF-A.;BFFFFFFFBFFFFFFFFFFFFBFFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1113:13532:8618/2 +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTGGAT ++ +CDDDBFFFFFFFGGGGGGGGGGHHHHHGGHHHGHHHGHHGGGGEHHGGHHHHHHHHHHHHHHGHHGHHHHHGGHHHHHFHHHHGCDCGHHHHHHHHEHHHGHGHHHGFHGGHGGHHHHHHHHFHHHFHHHGHHHHHHHHHFGGHHHHGGGEGAFHHGHHGGHHHHGHFBGFHGHGHGHGGHGGF@DAFEFBECAB=A.0BFFFEDF=A9.@D.-AAFFFA-:-..:.9/0:;0..-..0000::BFB09:: +@M01368:8:000000000-A3GHV:1:1113:21679:18011/2 +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCTGTCTCTTATACACATCTGACGCTGCCGACGACCGAGCTAGTTGAGATC ++ +BCCCBFFFFFFFGGGGGGGGGGHHHHHFHHHGHHHGFGHGGHGGHHHHHHGHHHHHHHGGGGFHHHHHHEGHHHHHHHHFGGFCGEHFHFGEGHHHFGGGGGHHHGGGEHGGGGGHHHHHHGDCCCGHHHHDGGGGCD/FCC->DFFF. +@M01368:8:000000000-A3GHV:1:1113:5741:16959/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF. +@M01368:8:000000000-A3GHV:1:1114:10130:11959/2 +ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGCTGTCTCTTATACACATCTGACGCTGCCGACGAGCGATCTAGTGGAGAGTTCTGTGGGGCCGGGGATCCTTATAAAAAAAATAGA ++ +BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAEEDG.CGCGHC0CGBFHGFBBF0ABDDEFF@?--:BB@.;:BF;0.0:0.0:000:BF.-.------.9/;000::0;0:--.000 +@M01368:8:000000000-A3GHV:1:1114:14540:5315/2 +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC ++ +CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/2 +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A.... +@M01368:8:000000000-A3GHV:1:1114:16639:15258/2 +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG ++ +CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0 +@M01368:8:000000000-A3GHV:1:1114:2404:13066/2 +ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACTGTCTCTTATACACATT ++ +CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFFFF.9//;FFFFF/BFFB/ +@M01368:8:000000000-A3GHV:1:1114:9184:6959/2 +AAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCCTGTCTCTTA ++ +CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHEHIHHGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGHHFHHHHHBGHHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHHHHHHHHGHGHGHHGGGGCFFFFFFFFFFFFFFFFFFFFFFFFFF.CFFFFAF=D=EAEFFF0B:0AF-DAFBFFFFFFFFFBFFFFFFFFFFBFFFEFF9B900B0 diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out1.fq b/sources/bin/tests/test-data/fastp_test/test-data/out1.fq new file mode 100644 index 000000000..0dde2858e --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out1.fq @@ -0,0 +1,8 @@ +@NS500713:64:HFKJJBGXY:1:11101:1675:1101 1:N:0:TATAGCCT+GACCCCCA +TAGGAGGCTTGGAGTACCAATAATAAAGTGAGCCCACCTTCCTGGTACCCAGACATTTCAGGAGGTCGGGAAATTTTTAAACCCAGGCAGCTTCCTGGCAGTGACATTTGGAGCATCAAAGTGGTAAATAAAATTTCATTTACATTAATAT ++ +6AAAAAEEEEE/E/EA/E/AEA6EE//AEE66/AAE//EEE/E//E/AA/EEE/A/AEE/EEA//EEEEEEEE6EEAAA/E/A/6E/6//6A@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE;>=EF?AEFFFF;9;=DAFFFFBBFFFBFFF//;BFB.:FBFFBB/BFFFF/BFFE?EFAFEF9 +@M01368:8:000000000-A3GHV:1:1104:11928:24197/1 +ACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATA ++ +CDDCCFCFFFBCGGGGGGGGGGHHHGHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHGGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHGHHHHGHHGHHHHGGHGEEGGGGFHHFHHHGHGEHHHHHHHHHHHHHHHHHGGGGGGFGGGGGGGGFFGGGFGFGAEFEFGFEAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@D9 +@M01368:8:000000000-A3GHV:1:1104:12288:20635/1 +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGCCGCAGCATCTGTCTTTGATTCCTGCCT ++ +ABA?AFBAB2>AFGGGGFFGD5GGHGFFHGHEGGGGHHHHFFHH5FHGHHHFFHEFHHHHHHGGHHHHHGFHGGHGGGGFHGGGFBHHHFGEGHHHHGHGGGGECEHHFHHGHHFFHFGGGHHHEGHDGHHGHGHFHHHECGCBCHHGFHHFHD1GFHEFHEF?GDCFFEFE0A@;@>BD/9BFBBBBFDFFFF99D=?>DDBFF-AFFEBB9BBEFEFAFFF//-@---;;FBBFBFB///;99999BA9 +@M01368:8:000000000-A3GHV:1:1104:13832:4398/1 +CACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTC ++ +AAABABCAFFFFGGGGGGGGGGHFHHHHHHHHHGFFHHGGHGGGGGHHHHHHHHHHFHHHHGHHHHHGGHGHGGHGGGGGGGHGFFGGGGDGGHHHHGGGGFGGGGGCFGGEGCDGGGGGGGGGGGGEGF?;BFFFFFF +@M01368:8:000000000-A3GHV:1:1104:23670:4161/1 +ATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCC ++ +AAAABFFFFFFFGGGGGGGCGBBGGHHHHHHHHHGHHHHHHHHHHFGGHHHHHHGGFHHHHHHHGGGGGFHHHGHHHHHGHHHHGHHGGGHGGGGHHHHHGHHHHHHEGGGFHHHGFFDGEGHGHFHGHHGEGGGHHBGHGGHGHGGGGG/@FCDFDGFHGGGDFFHFGFFGGGGGHHHHGGGGGGGEGCDG?GGBFFFEE00BFFGABBBAFGGGEGEA.9FFF/./;BFBF./AAF/BFFBBF/F/BFB +@M01368:8:000000000-A3GHV:1:1104:24927:22253/1 +AGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTAT ++ +AAA?AFFF3DFFFGGBGFF3EAEEEHFHHFHHHGHHHHDGHHGAEFGHHHGFCHHGHHHBGHHHAEGGHGGFHFBFHHHHHHHHHHFHH1EEHEEHH1FFDEEFCGHBGHHFHEHHHHHH1FCGHHHHEEFGEEGFFCHHH11>GHHF/FG2DGGCGAGGHGGGG@@@BEFFF?@@@FFEFFFFFF?@@FB@BB@FFFE=;==---A9EFBBB/;E;A9B/B/FFFEF/B///;/;9/A/;/9BFFFBFBB +@M01368:8:000000000-A3GHV:1:1104:4705:7727/1 +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +BBBBBFFBFFFFGGGGGGGGGGHHHGHHHGHHHHH6GHHHHFFGGGHHHHHHHHHHHHHHHGGFGGGEGGGHHHHHHHHHHGHE3FGGGGHHHHHFHHHHHHHHHHHHGGGGGHHFHFCGFHHGGGGGGGHHGGGGHHGGGGGGHHHHGGGADCHHHHGDGGGGGGGGC@DGFHEHHHHHHGHHHHGFGDEGFGFFGGGGCFGBEGFGGGFG;C.BFFFFFFFBFBFFFF/F?.AFFF/BFFEFFFFFEFF +@M01368:8:000000000-A3GHV:1:1104:7756:4776/1 +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +CCCCCCFFFFFFGGGGGGGEEFHHHHGHGHHHHHHGGHHHGGGGGGHHGHHHHHGHHGHHHGGFHHHHHHHHGHHHFHHGHHGFGGGGHHHHHHHHGHGHFFHFHHHHHHGGHGFGFHHHGHG?FGHHHHHHHHHHHHHHGHGHHGHGGCDGFFHHHHGHHHHHGHHHGFHGHFHGHGHGH/@CABFFFFFFFACAFF?BBFFBFD-@-.D>FFAF.F.:9---;AADFFFFFBEFFF:9FFFFBBFFFF/ +@M01368:8:000000000-A3GHV:1:1105:11310:21761/1 +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTT ++ +CCCCBFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHGHHHHHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHGHHHGHHHGHGHHGHHHHGGHGGG=FFGEHHHHHGHFGGHHGHHHHHFHHHHHHHGGHHHHHHHGHEHHGHHHHHGGGGF9AGE?DEGFFGGGGGGGGGGGGGGFFFF/9FFBFFFFFFFEFFFBFFFFFFFFFFFFEFFF0 +@M01368:8:000000000-A3GHV:1:1105:11578:14676/1 +ATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTC ++ +CDDDDFFFBFFCGGGGGGGGGGHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHFGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHHHHHHHHHGHHHHGGGGGGHGGHGHHHHHHH;CHHHHHHHHHHHHHHHGHGGGGFGGGFGGGGGGGGGGGGFGGGEGGFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1105:13575:19255/1 +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGTTCCCGTGAGTGGTTAATAGGGTGATAGGCCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG ++ +AA1A1DFFFFFBGG3A111FFAEGDDBGFDHF00F01BBA00BFGEHFBFFA1FABB0FAE?CFHF1BGFHFB0011F121E//>>1F10>B?EFHGCC/?/BFG/EEGFFEE//BCFDE0?E@@B/?11AAFFFFFEAGGGFGGAA6FHDGGCGFHFFHFHFHHHHHGDDDFFFHGFFHGBEGEGHHHFFFHGEEAEGHHHHHFHHHFHGHFEDGGEGBEAGEFHHFFHHHHHHGGHHHGHHGBGHHFHHFGHHHHG?CG?AFHH1FHHHGHFHHHF?DGHFFHCGAGEFHGCBBBB?BFFF?B-B.9/BFFFFFB=-AD?..@FFFF@@-@@?AFD.FFFBBEEBD9/:FFFFFBB/:FF9BF/BF.BBFF/: +@M01368:8:000000000-A3GHV:1:1105:21099:2895/1 +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTT ++ +CBCBBFFFFFFFGGGGGGGGGGGGGFHHHHFHGHHHHHHFHHHHFGFHHHHHHGHHHHHHGHHEHGGGGHHHHHHHHHHHHHHHHHHHHHHGGHGGHHHHHHHHFHHHHGHGHHHGGHHHHHGGHFFGHGCGGGHGHHGHHHFGHHFHH/FGGGHFGFEGGCFCCD;B@DFFFFFFFFFFFFFFFFFFFFFFFFF;F.BEFADFFFF.AEFFFFFFE;D.;:B00099:09BFBFFBFF.0:000BFFBF0 +@M01368:8:000000000-A3GHV:1:1105:26469:19245/1 +TTATGATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCAAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG ++ +BAAAAFFFBFFFGGGGGGFFGGHHHHHHHHHHHHGGHHGHHHGGHHHHHHHHHHHDEGGHGHHHHHGEDHFHGFHGGHHGGHGGEHHHGHHGHHGHHHGGEGGGHGHGHHHHHHGHHHHGHGGGGGHFHGGGGHHGGGGCDGHHHGD>A@FFFFFFFGGGFEECFGGFFB5GBHH5DFH5GBEEAEFHFHHF3F3GHFHHHEF3GAEHBGFHFFEFFHHHHFFB31FGGEGFHGEHHHHHHHHHHHHHHHHHEEEEGHHHFFF3GF3FGF44BBGEHHHHGG2B/BGGHE;B=.9.;.BBFFF..;A;/B/;B//;;//BBF/ +@M01368:8:000000000-A3GHV:1:1106:22927:3863/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGACTT ++ +A>ABAFA?D@AFGGGGFGGGFGFHHHFFH4BCBGHHHHGFFF3G5BF3322EEAFHHHHHHAB5GHFHEHFHHH3BEEHFGF5@13FDF3GDGFHHFGHHHGHHHGFGGHHFCG//?/EGHHHG3F4BFFGHHHEDGFHHB/B/?FBF<@-9?BDEFFF?B--?DFFFB9FA>B;A.BFDB?AB.--@;-.FFAEFFFF9AE;DDFFFFB/9BF +@M01368:8:000000000-A3GHV:1:1106:23625:4236/1 +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTA ++ +@?AAAFFBFBFFFGGFGFGGGEFCGGHHHHFGHGHFHGHHHHGGFGGFGHHGHGHHHHGHGFFHHGGGGGHHHHHHHHHBFHHEFHHHHHHGF?FAGHGFHHHGDGFHHGGGHGHFHHHGHHHGHHFHHGFFGFHHHGHHHHFFHHHHH/FGHHHHGHGHGBFFF9 +@M01368:8:000000000-A3GHV:1:1107:14451:26748/1 +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BABBBFFDABBBGGGGGGGGGGHGHHHHGAGHGGGGGHHHHHHHHGHHHHHGGGGGGFFHHHHHHHHHFHHHHHGGGGCHFHH3FEHHGCGGGDGHHHGFGGHHGGGGHHHHHHG/DGGGHHHHGGGGGCCHGG?CGG1GHHGHHHHBGHHHFHHGHHHHGGADAD00ECEGHEFHHFFAEFFFFFGGFBFBFFFGFFG.;B/99;BCFGGGGEFFFFFFEDA./:ADEB?FBFFFF;FFEBFBFFB./9. +@M01368:8:000000000-A3GHV:1:1107:18714:24788/1 +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BBBCCFFFDEDEGGGGGGGGGGHHHHHHGGHHGGHGGHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHCFGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHGHHHHHHHHHHHGHHHHGGEGEGCCEGGHHHHHHG:CAFFGGGGGGBFEFGGGGHGAFFGGFGGGGGGGEFFFFFFFFFEF/EDDFFFFFFFFFBFFFFFBBFFBBF/ +@M01368:8:000000000-A3GHV:1:1107:21355:8333/1 +ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +ABCBBFFFFFAFGGGGGGGGGGHHHHHHHHFHHHHHGGGGGHHHHHHFHHHGHHHHHHHGGGGGHHHHFFGHGHGGGGGGGHGGEGGGHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHGHHHFHHHHHHHHGHFFHHHHGGHGEGHHGHGFHHFHGHCEFHEGHGHHHGHHHGGGGGGCFFFFBFGGFGGGGFBG?FDGGGEGFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF.AA/9 +@M01368:8:000000000-A3GHV:1:1107:22864:15712/1 +AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTAC ++ +BBBBBFBBFFFFGGGGCEGGGGHGHHDGFHHHHHHHHHHHHHCHHGHFGBGDFGE?GHHGHFBHHFHHHHHHHHHGHFGFGHGHHGGC@DCFGHHGGGGGGGHHHHHHGGGGGFGGGGFFGGGGFADGFEFFFFFFFFFFF9;FFFF/BFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFEAECDFFFFFFFFFBFFFFF +@M01368:8:000000000-A3GHV:1:1107:24817:14233/1 +CTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACAT ++ +3AABABFFBFFFGCFGGGGGGGHHHFGCFGGGFFGHHCGHHHGHGHGHBFFHHHEDGGFGFGHHFFFHGGEGHFHHGHFHGFFHHHFGHHHFHACECEHHHBGFHGFHHHFHHF4GFHFHFHEHGGE/EG:A-CFGGFGADGGGGFGGGGDAAAADFA.-AFFECFDAAFFFFEFFFFBFF;D;BFFFB/;BFFFFFFFFFFFFFFBFFBF/;//;BFFFF?FFFFFFEDAFFFFFBF//:BFBACF--9/ +@M01368:8:000000000-A3GHV:1:1107:24830:14440/1 +AACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +ABBBA@FFFFBBGGGGGGGGGGHGHHGHHGHHHGGHHHHHGHGHHGDHHHHHHAGGGGFHHGHHHHHHGHHHHHHHHHHHEGAFGFHFHHHHGEGHHHHHHHHHHHHHHHHHGGHHHGEFEGGHHGHHHHHGGHGFHH/?GHHHHGFGHGFHCGGBBDAFFFEFFFFFFFFFFFFFF=CDDADDFFFFEF=BFFFEFFFBFFFFEEBF./:FFFFFFFFFFFFFFFFFFFEFFFFFFFFFFF/BFBEFFC- +@M01368:8:000000000-A3GHV:1:1107:26478:23602/1 +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +1AAAAF1B13BBBEGGGFGGGGGGHHDB1BGFHHHFGFGGG0F00BGBGFGGF1GBGB1BGCGAEE/FGFHGHFHHHHHBFF1B0FGGF//F//FGFGFFF/1@B1DFHHHGGEFEDHFDFAFF0B//1FDD1GFFHHDF?1BD>GF/GCAC0C@?@-;99BBB->@--;-B//99B--9-BF=A--A-:A----9AA9AFBFBBB?E@BBFFFFFFFBFFFFF +@M01368:8:000000000-A3GHV:1:1108:11059:23181/1 +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGAT ++ +CCCCCFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGHIIIHHHHHHHGHHHHGHHHGGHGGHHHHHHHHHHHHHHGGGGGHHGHHHHHHHHHHHHHHHGGGGGHHHHHFGHHHGGGGGGHHHGGGGGHGGGGHHHHHHGGGGGGHGGHEFGGGGGHGGG-ECHHHGGGGGGGGGFGFFGGGGFGGGCF?EFGG0;BFFFFB?9AAFFFFFFBF;BBFFBFFFFE?F/ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/1 +TAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +BCCBAFFBCCCCGGGGGGGGGGHHHHGGGGGHHHHHHGHGHBGFHHHHHGGGGGHHGGBFGHHGGGGGGGHHHGGGGHHGGGFHHHHHHGGGGGGHGHHGGGGGGGGGGGGGGHHHHFHHHGHGHHHHHHGHGHHGGFGGGDFFGGHHHGHGH/FHHHFHGHGHHGHHHGHHBAAAA3BDFFFFDGBFFEEGGGGHHGHFHHCFHGHGHHHGF3BFGFHGFEFHFHGH3EGFC1EEGBFGBHFGGFFHHHGHFHGHHGHGGHCEHEBCFF3ED3@GH4FDEG12FFHFFHG/G3FGA/@EFEFCG33FFGBBGHFHH/?BFBGFGFAGC2C/@-;@-;BFFEFADF?DFFFFFF?;AFFA;AD;..FEFFA--;9;D.9BFFBE?;.;///://///99//BB/9;F./B//BBFB9// +@M01368:8:000000000-A3GHV:1:1109:25237:11722/1 +CCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG ++ +AABBBFFFFFBBF5BGGFGABGHGGAEFGFHHHHFHCHFHHBFGGGEHBGGHFFFFGFAEF5FHH?EGGF5AEG3?EBFHD?C/EFHFFEGEE?CFGGGHHFHB3EEFG?EEGHCFGGGGGGGECCFHHGDFGGGGGEFGC?EGHHHB0CGHHGCGHHHHBEHGHH.::ACA;FECFGGGGGFFFEFGGGGGGGFFBBBFGBFFFEFFFFBFFFFFFBBFBFFB9..AF?FFFFF +@M01368:8:000000000-A3GHV:1:1110:14751:26540/1 +TAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACTGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGTTGTGCACGCGATAGCATTGCGCGACGCTGGCGCCGGCGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG ++ +AAA?1CFFFFADGEEGFGB1112DGDGHGFGHHCG/ECEBGGHDFGHHFHGHEB1BCGFFE2EGHHGHFFFHHBFFHEFCGGHHFHHHHH111BFFHGHEHBEHGGECEFHGFHFGGDBBGHHBHHHH0GH22FGHGFFFH1BFCG0F@FGG11@GDHFG1D/1FGFHH/FCG.>0><-<@CCFFG.CC-@C?C9FFF0C---;------;9----9-9@-AAFF9B9---9-/;B9BF/9BB//B/;/// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +BBBBBFFFFFFFGGGGGGCBGGE?GGGHHHHHGHHBEGGHHGGGGGHHHHHHHHHHHGGHHHHGFGGGGHGHGCFGHHHGGGCGGHGHGGGGGHFGGGHHHHHHGCEFGGHHHHGGGGGGGHGG/CEGHHHHGFHHHGFHHGFFHGHGHFGGEGFDDGGBCGHHGFHH/CHHHHGHGHF0CFGGGGGGGFFFFFBFFFFFFGFFGGF?DGEDEEFEFFFF?FFFFFFFFFFFFFFFBFFF.BFFFBFBBA; +@M01368:8:000000000-A3GHV:1:1110:16559:7507/1 +CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAACTGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +ABBBAFFFFFFFFGGGGGGGFGGGGAGHHGCHHGHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHFGGGHHHHHHHHBDHHHHHGGHFEEGHGGHHHHHHHGHHHEHFGGGGGGHHHF33FGHHG3GDDGH//EEGHHFFBF?GHHFCC@DGFCGGB?DGHAFGGHHGFH0E??<@DGHGGCFGGF?DGGGFFGGGGGGGG.C/0BBF?FBBEGG0FFF.AA9;B9/E////99;;:.//:FFFFBBF//9 +@M01368:8:000000000-A3GHV:1:1110:16700:6843/1 +AAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAAC ++ +BBBBBFFFFFFFGGGGGGGGGGHHHHGHHHHHHHHHHHHGGGGGHHHHHGGHGHGGGGGGHHHGFFGHHGGGGHHHHHHCGG@FGHFHFEGGGGGGHGGGGDGHHHHHHHHHHHHHHGHHGHGHHGGGGGCGHEHGHHHFHHHFF.DGHHHHHHGHHHHHHGFGHGCGHGHHHHHHHHGHHHCD?:A::FCDGEGFGFFBFGBFGGGF00CBFFFF/BFBFFFFA +@M01368:8:000000000-A3GHV:1:1110:18014:7856/1 +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG ++ +AABBBFFFFFFFCGGGCGGGGGGHHHHHGFHHHHHHGHHHGGGGGFHHGHFGGHHHGGFGGGHHGGGGGHHGGGGHGGHHHGGGGGGHHGHGDGGGGGGGGB/ACC=@--AFBFFB?=BFDFFF//FDB;-9A-AD-.A.A=?-9-:B/AEB/BFF.A;DDFFFBBFFFF/BBFFFFBFF9B; +@M01368:8:000000000-A3GHV:1:1111:13195:14562/1 +ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC ++ +ABAAAFFFFFFFGGGGGGGGGGGHHGG4FDFGFGGCGGGHGHG?EGHEGFFDHFHHHHGGFE@EHHGEEEGFCCEFFGFG/EHHHHHBFBGGHFHFHEHGHEFGGGED/EFDEFFEHHBGHHCFFFDFGGHHGFFFHHHHGFG>0<0DGGFHBGHFBDFGHGFFGGAGHHGCGBHFFHHHFFFBFGGGGF/:FFFCB9F9FF0FEFE?FF0BED-D./ +@M01368:8:000000000-A3GHV:1:1111:14287:20817/1 +GCCAACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTCATCGCACCTACGTTCACTATTACAGGCGAACATACTTATTAAAGTGTGTTAATTAAT ++ +>>A3>AAAACFFFGFGFGGGGGHGHHHHHHHGGGGGHGHFFCGHHGBGHFHHHHAGHHHHEHHAGFFEHEAE?GHHHHEGFFFDGHGHBFFHFHHHGHGHGHBECG@@@EHGGEGCGGGGFFGGGG?BGGGGGG.-C.FEDCFFFEFFFAF/99BEFA.:9BFB/9FFFEFFFFFFEFFF/FBBFFFFFFFFFFFB//;.@@//;DFFFF//BBFFFBF;A;DF=>B//;9B//B/;/;9//9//;B/:B9 +@M01368:8:000000000-A3GHV:1:1111:23624:14516/1 +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGGGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAG ++ +3>3AAFFFFFAFGGGGGGGGBGHHHHHHGGHGGHEHGHADFHHHHEGGGHBGHFFHHEHHGHFHGG5FBEEGEGHHHGHHHEFDGHHFFGFGGHHGHHHGHBHGHFHFHHGGGGFCFBGFGE?GFBECEGDGHEHGDGCGHGC/DF@GHGFFCGGGGFFFFDD?@C@GFEC?-ADHFFHBGHFBHFG0CC//.;B0/CA.;AA.;@.AB/9BB/A/.AFFFE/BFFF///9B/FBDE9/;99/B/BFFEF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/1 +ACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGT ++ +CBCCDCFFFFFFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGFFEHGGHHHHHHHHHHHGHHGGGGGHHHHHHFHHHHGHHHHGHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGCGHHHHGHHGHHHHHHHEDHHGHGGGGGD;BEGGGFFGGGGC:CFGGGGGGGGGFGGGFFFGFFFFF; +@M01368:8:000000000-A3GHV:1:1111:8665:25542/1 +TCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTGTCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +AA3AAFFFFFFFGGGFGFFGGGGHGH4AGGGFHHCGEE2FGHHHHHHHHHHGFHGF53FHEGGFAF5CFHHGGFGHFHHGGHHHCHHHHHHHFHHGH?EEEG1FFFEHHFHFGGHHGG?F4FBGHGHCHEF0//-9--;0CFGG?@BGDGFFFFEFBBBDA?FFBFFFF=B;-9.AA9EFFFF/;9BD.//;9/9/B:/:BFBFFBFFF/B:BFF//;/B/FFFBFF.A-BFFFBA/F//BFFFBF/;/A- +@M01368:8:000000000-A3GHV:1:1111:9655:13916/1 +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +1>>1AAFFFFFBGGFE1EEEEGGHGHHH2FGHHHFGFGHGCFGGGEFHGGEGGHHHHGHEFBFEGHHHGHHBEHHHHGHGFHHHGGGGHHEGGGGHHHGFHGHHHH1FHHG?G/AGF1GBFGEFFHF2FDD0FG--99@=---AAABA-BF/B?A@F-9BBFF//BB/9/ +@M01368:8:000000000-A3GHV:1:1112:10272:7828/1 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAC ++ +AAABABBBBBBFGGGGGGGGGGHGHHGHGHHHHHHHHHGHHHGGHDGHHHGGGGHHHHHHHHHHHHHHHFHGHHHHGGHGGHHHFHHHHHCGHFFHHHHHHHHHHHHHGHGEFGAEEEEHHGHHGHGHHHHHHHGHHHHHHGHGHFFBC/BA?BGGGFFFFFFFFFFFFFFFC-@DDFFFFFFFEFAFFFFF +@M01368:8:000000000-A3GHV:1:1112:9832:16531/1 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC ++ +AABABFFFFFFFF4GGGGEBGEFGHGGHGHGHHHGGHFBGFGGGGGHHEFHGEHFHFHEHHHHHGCGGGHFHHCFGHE@1EEEFFGB?EEEEHBGGGCHHGHHBEE@>EAHHFAEBDGGGCEFF?CEGFFHHHHHFHHHFHGHCGCAHHF<..C.D=0CD.GFHHHG.CAGHC:CHB0GGGFFB0:CFA.A-;9.;000CBBFFBFGA.9AA;A;EDDE.ABBFFFF9;BEFFF/BF//9/B//9:B//.. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/1 +CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA ++ +AABBBBFFFFFFGGGFGGGGGGHHHGGHGGHHHHHHHHHHHGHHGGGGGHHHHHHHHHHHHHHHHHHGGCGDHHHHFGGHHHGGGGGFGGHGGGGHHGGGGHHHHHHGGGGGGHHGGGGDGGFGHGGFCDCHHHHGHHHHGHHFAGFGGEHFGEG.C1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF +@M01368:8:000000000-A3GHV:1:1113:5741:16959/1 +TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA ++ +ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BFFB/B9B/9 +@M01368:8:000000000-A3GHV:1:1114:14540:5315/1 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT ++ +AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/1 +TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA ++ +BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/; +@M01368:8:000000000-A3GHV:1:1114:2404:13066/1 +TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT ++ +CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out_bwa2.fq b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa2.fq new file mode 100644 index 000000000..bb1615d22 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa2.fq @@ -0,0 +1,388 @@ +@M01368:8:000000000-A3GHV:1:1101:14518:9998/2 +CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA ++ +CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0 +@M01368:8:000000000-A3GHV:1:1101:18422:19051/2 +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF +@M01368:8:000000000-A3GHV:1:1101:25545:21098/2 +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT ++ +3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<.<<AABBFFCFFFGGGFGGGGGGGGHHHHHHHHHHHHHHHHHHGHHHGGEGGFFHHHHHHGHGHGHHHHHEHFHGHHHHEFHHGHGGGGGHHHHGHHHHHHHHHGFGHHHHHGHGHGHHGGGCCGGGGFGGGGGGDGGGGFGDGGGFFFFFFEFFFFFFFBAF:9AF//;BEF-DD/FFFFBFFFFFFFFFEBFF?FB;/;//BFFEFFE/::..9;-:B9:FBFFFFFF +@M01368:8:000000000-A3GHV:1:1102:17584:10050/2 +GTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +ABCCCFFFFFCFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHFHGGHGGHHHHHHHHHHHHHHGHHHGGHHHHHHHGGHHHHGGGGGHHHHHHHHHHHHHHGGHHHHHHGHGHGGHGGFGGGGGGGGGGFGGFGGGGGGGGGFFFFFFFFFFEFFCFAAFEFEFFFFFFFCFDFFFFFFEFFFFFF +@M01368:8:000000000-A3GHV:1:1102:18842:24844/2 +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +CCCCBFFBFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHFHHHHHGHGHHHGGHGGHHHHGHHHHHHGHHGGGGGHFHHHFGHHHHHHHHHHHGGGGGHHHGFECGGHGGGGGGHHHGGGGHHGGGGHHHHHEFDCADGHHHHGGGGFC?AE-@DDFHFFHHHCFHGGFFGFFFGGGEFEGFGED9C?CEGF90FEF/A./BBF9FFFFFFFFBFFF.9AF////;FFBFFB/:BF +@M01368:8:000000000-A3GHV:1:1102:21788:11027/2 +AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGC ++ +CDDDDFFFFDDFGGGGGGGGGGHHHHHGGGGHHHHHHHHGHHHHHHHGGHHGEHGGHHHHHHHHHHHHHHGGGGEHHHHHHHHHHFFFFFHHHGGGGGHFHGBFEHHHGGGGGGGHHGGGGHGGGGGHHFHHHGGG@CGHHHGGGGGGGGGGGEGDGFFDHHGEHHBCFHGBGFAGGHFGGCEEF0BE///FDFACF?FHFGC//??1B0<FF>DFCFDFFFFFFFFF-BBAFFFFFFFFE@D9B;FBFFFFF +@M01368:8:000000000-A3GHV:1:1103:25465:20010/2 +AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCACCCTATGTC ++ +AAABBFFFFFDFGGGGGGGGGGHHHHHHGHHHGFHHHHHHHGGGGGHHHHHGHHHHHHHHEHHHHHGHGGHHGGGHHHHGGGGGHHHHHEHFGEHHHEE14BGHHHGHGHFCE/EFGGGGGGHGGGGGG?FFGGGG.ADGGGFFDA.FFEC--;9BBBD?FFFFF +@M01368:8:000000000-A3GHV:1:1103:25519:6301/2 +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATGCTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGATGTCTTATTT ++ +>AABBFFFFFFFFFFGGGCAFGCGHGGGHGGGHHFHHHFHHGGGGGFFFHHHBHHHHG5BG5GFEEEE1FGFFGF1EGHGGG/BFHEF@EA1BE1@EED3?4DHGGGGEGHFFFDDG?DCDEG@<?@DGCAGC-;@DGFFHGCHEEFGGFGFB/;..BBB.CCE?A0FE0EBFF0FEF.;=DFFB//BFBF//;/:9BA.9FB9//;9//;9F;FF +@M01368:8:000000000-A3GHV:1:1104:13832:4398/2 +GACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTG ++ +BBCCCFFFFFFFGGGGGGGGGGGGGHGGGGGGGHHHGFGGHHFGGGHGHHGHGFGECGHHHHGGGGGGGHEGFGGGHHGHFHHHHFGHFHHHHGHHHHFGGFGG3FFGGHHHHHHH2?FFGHFHHHHHHHHHBGHDGC0 +@M01368:8:000000000-A3GHV:1:1104:23670:4161/2 +CGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAA ++ +A3AABBFFFFFFGGGGGGGGGGHHFHHHHHHGHGHHHHHGCHHHHGGGGHHHHHHHHHHHHHHHGHHGHGHGGHGGHGHGGHHGFGHHGHHHEHHGHHHHHGHEHEHHHGGFGGHHHFHHHGHHHHHHHGHHHHG4EGGGFCBBCA?DGGGGGGCCAFFFFFFFFFFFFFFFFFDFFF.9@--=AFFFF;FBFFBEFFF9FBFFB9/FFFFFFB/FFFFFFFBFFFF/BBFBB/FFFE?.;@FFB?FBB// +@M01368:8:000000000-A3GHV:1:1104:24927:22253/2 +GTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGGGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACGAG ++ 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+BCCCCFCCCCCCGGGGGGGGGGHHHHHHHHGGGGGHHHHHHHHGHHHHHHHHHGHHHHHHHHGHHHHHHHHHHGGGGGHHHHHHHHHHGHHHHHHHHHHHGGHGGHHHHGHHHDGHHHHHHHHHHHHHHHHHGHHHHHGGGGGGHHHHHGHHHHHHHHFFHHHHHCCAHFHHGGFFFFFFFFFAA;BDDFFFF00.-=D.ABDA-.::AAF;F@.AAD./0000.9-;.9:00009:F090;FF000900; +@M01368:8:000000000-A3GHV:1:1105:11578:14676/2 +GCTCCGGGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGT ++ +CCBCCCBBCCCCGGGGGGGGGGHGGGGGHHHHHHHGHHHHGHHHHHFFFGGHGHHHHHHHHHHHHHHHHFGHHHHHHHGHHGHFHFGHHHGGGGHHHHHHHHHHHHHHFHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHDGGCGHHHHHHHHHHHHHFF>ABFDCFFFFFDGFGFDGDEG1EGEFFBFHFGHA0E00A0CAAC0FFDFFAGHFEHHFDH/EAFCFFHACGHHAFFEF2DFFG/FGHHHHGHGH0C@/E@GGC0FG10>GGFGHHGHFFBGFGB2>F@;-A@FF<-;---@-;-----;-BFF/;---9//BBFFFF//B;FF///9BF///;/;B/BBFBFFBB/;-9--///;9/:-;BFFBBB9F +@M01368:8:000000000-A3GHV:1:1105:15502:11453/2 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+CCCDCFFFFFFFGGGGGGGGGGGHHHHHHHHHHHGGGGHHHHHHHHHHHHHHFHHHHHHHGGFGGHHEHHHHHAGHHGHBHHHGHHHHHHGHGHGHHHGGGGGHHHHHHHHHHHHHHHFFHHHHHGHGHGHHGGGACAFGGGGGG-AFGGFFFFFFFFFFFFFFFFFFFFF-9@AFEDFFFFFB.9-AABBBFFFEFFFFFFFFBFFFFFFEBB0BBBFFBFFBFBEDEAFFEB.ABFBFBFFFF0::/.- +@M01368:8:000000000-A3GHV:1:1105:17564:15723/2 +ATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTT ++ +CCCCCCCCCFFFGGGGGGGGGGHHHHGHHGHHHHHHGHHHHHHFHHHHGGGGHHGHFHHHHHHHFHHHHHHHGHGGHGGHGHHHHFHFHHGHHHHHHHHHHHHHEHGHHHHHGGGGGHHHHGEHHGHHHHHHGHFGHFHGGAHGGHGGGCCBDFGFFAFDBDDFFFFFBDA;AAD-ADC?AFEFB-@@AAEFEFFFFF..-:.B0:FFFFFFEF0BFF09FF.0;9BFFFFF0BFFFFFF?.::-909;.9 +@M01368:8:000000000-A3GHV:1:1105:18108:12091/2 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+CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHGHHHHHFHGHHGHHHHHGGFGHHIIHHIHHHHHHHFHCFGHEEHFFHGHHFGHGHGHFHHGGGGGGEEGHHEHFHHGGHFHHFGGGGDFGBCGG?DGHGGFCGGHHECEF?CHGGDGFFGGHHC?EEGGHHHH.>AEGGGHEE-AEG0C0GCCEFFFFGEFG/;CEGGGE.:CAE.;@.@EFBFFFF/..:BFF0:BB00FBFFFFBDAFFF0;0B +@M01368:8:000000000-A3GHV:1:1105:20577:18421/2 +ATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGCCGAAAATACCAAATGCATGGAGAGCTCCCGTGAATGGGTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTT ++ +?ABBBFFFFFFF4CFFGGGFGGHHHHHHHCEGHHCHFGHCAFEFHHHGGAEGGHHDHHHBGHBGHHH?5BGE1AEEFHHHHHGHFHBGHGEGGGGHBFHHFGHBGCFFG4EGHGG?E/FG3F3F/FGCDECEA/FGG/CEDBB//?BHEHHF0ADC@D>D9@DDCFFFFFFCFDFE.AA;/BB/.;-.;BFBBBFFBFFFFFFF/9FF?/;/BBFFFFF/;FFB/ +@M01368:8:000000000-A3GHV:1:1106:17389:18671/2 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+BCCCCCFFFFFFGGGGGGGEGGHHHHGGFFHHHHHHHHHHGGGGGHHHHGHHHHHHHHHHHHHFHHHHHHHHGHHHHHHGHHHHGGCGHHHHHHHHHHHHHHHGHHHHHGDGHGGHHHHHHHHGHHHHHHHHHHHGHHHHHHEHHHGHFGGGGHHHHEHFHHGHFHHF.>GGHHHGHGHGGHCFFCDFDFFFFFFAAF.FFFFFEFAFCFFA..@.AFFFC9--9;.;A///00--;A-.;.000000090 +@M01368:8:000000000-A3GHV:1:1107:21355:8333/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCGGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +AABCCFCCCCCFGGGGGGGGGGHHHGHHHFHHHHHHGHGHHHHHHGHHHHGGGGHHHHHHHHHFFHHFHGHHHHHHGGHGGHHHGHHHHGGHFHHHHHHHFHHGHHGEFFHFHHGGGGGGHHHFHHHHGHHHHE?FGHHHHGFGHGHHGGGDGGGGGFFFCFFFFFFFFFFFFA;DBBDFFFAFFFF;DBAFEDFFFFFEA?-9...9;9;BFFFF//BFBFFFFBFBFFFFFB/BFFF9B/EDEF-BFF. +@M01368:8:000000000-A3GHV:1:1107:22864:15712/2 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+CCCCBFFFFFFFGGGGGGGGGGFHHHHHHHHHHHHHHGHHHGEHGGHHGHHHHHGHHEHHGGGGEHGHHHGEHHGHHDGHHHHGGGGGFGEFGGEGHHGCEEEGHHEFGGDHGGGGAGFHHHHGGF/?//GHFFDGGGGGHAD??DC1DHHBGHHHHGHF<FGGGGGGGGGGGFHHEFGHHHGGGGGGHHHCGGEFHFGGGFHHHHHGGGEGGHHFHEEGEG/EEEE/?/EHFHH3GGH4EGHHCB01CGHGHGD//<@CGGBFFDGHHHH0FEHHGEGFHCD11>0=GGHGCCFGHGBGGD0GGHC0C.@?ACEEC/.EDEB?BFFCFB9CFF090BBCBFBF0CCB0B00A.9E.B/9BA=-..B9FBF//;BBBBFF +@M01368:8:000000000-A3GHV:1:1108:11059:23181/2 +AACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +CCCCCFFFFFCCGGGGGGGGGGHHHHHHHHHHHGHHHHHHHHGHHHHHHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHGGHGGHHHHHHHHFHHHHHHHHHHHHHHHHGHGHEHHGFCGGGHHHHHHHHHHHHHHHFGHHHHHGHGHGHHGGGBFGFFFFEAFFFA.BFFFEFDDFFFFFFFFFFEEFF;D;EFFFFFF0BFFFADDFFFFFBFBFFFFFBB0FFFF0::0BF000BFFFBBF0EDFF@ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/2 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+ABBBBFBBBBBFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHDHHHHGGGGHHHHHHHHHHHHGHHHHHHHHHGGHGGHGGHHHHHGHHHHHHHHHHHHHHHHFHGHHHHHGGGGGHHHHHGHGHHHHHHG?FHHHFHGHGHGHHGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAFFE.ADEFFFFFFFADFFFFF///BBFF/FFFFFBFAFFFFBB///;9: +@M01368:8:000000000-A3GHV:1:1108:16350:22621/2 +CATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATAT ++ +CCCCCFFFFFFFGGGGGCGGGGHHHHHHHHGHHHHGHGHHHHGGGGHHHHHHHHHHHIHHHGHHHHHHGGHGGHHHHGHGHGHHHHHHHHHHHGHHHHHHGGHHHHGGGGGHHHHHHHHHHHHHGHGHHHGHHGGGGGHHGGGDADDGFFGGGGFFFFFFFFFDFFFDFFFFFFFFFFFAFAEFEDFFFFFFEE-AAFFFFFBFFFFF0FFFBFF;AFFFFFFFFFFFFFFFFFFFFFAB9BFFFFFBFFF +@M01368:8:000000000-A3GHV:1:1108:21791:23272/2 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+BBAAAFFFFFFFGGGGGGGGGGHHGDHHHHHFHHHHGGGGGFHFFGFFHEGHHHHHHHHFGHFHHHHDEHHHHHHGHFHHGGGGHHGFHHHHHHHHHHHHHHHHHHF?EEFCHFGFHHEFFFHGFHHGHFHFHHHFFHAG??GHACGGDGHGGBFHHHHHHHGHFGHGHGEGHGCFFF@CD-BDDFFFFFFFFDDFFBBFFD-B-A.DFFA.AFEFF-;-..:..BFFFFFA-../9FFF//B/BBBBFF/ +@M01368:8:000000000-A3GHV:1:1108:25084:18127/2 +CCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAG ++ +CCCCCFFFFFFFGGGGGGGGGGGGHHHHHHHHFHHHHHHHHHHHHHHGGHHGHHHHHGGGGFHHHHHFHHHHHHHHHGGHHHHHCGGHGHHGGGGGGGHHGGGGGGGGHHHGHHGGGGGGGGGGGGGGGG@CDE?EFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFE;DFBFFFFFFFFFFFFFFFFFFFAFFFFFFFBFFE0BBBFFFFFFFFFFBFFFF9BB0:0:B; +@M01368:8:000000000-A3GHV:1:1108:7626:10048/2 +AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +BCCDDFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGHHHHHHHHFGHHHHHHHHHHHHGHHHHGGFHHHFGGGGHHHGHHHHHHHHHHHFGHHHHHGHGHGHHGCGCGGFHHHGGGGGGGGGGGGGGGGGGGFFFAFFFFFFAA-AFEFFFFFFFFFFFFFFFFFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1109:11270:12255/2 +CTACCTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATT ++ +BCCCCFFFFFFFGGGGGGGGGGHHHHHFHHHHGGGGHHHHHHHHHHHHHHHHHHHHGHGGHGGHHGHHHHHGHHHHHHHHHFHHHHHGHHGHHHHHGGGGGHHHHHHHHGHHHHHH?FHHHHHGHGHGHHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFECADFFFF.DEBFFFFFF;D.B;.ED.FFFFFFF-.:00009BBF +@M01368:8:000000000-A3GHV:1:1109:24217:19077/2 +TAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGAACCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTT ++ +BBBBBFFFFFFFGFEGGCFGFGHHHHFHHFHHHHHHGGEEEFGHGFFAGFFEEAEGGHHBEEFAFGAEF1G3GFGGEEF@EAGGHGFF?ECGGHEEEFGGHHHHFHHFHHGFHHHC2DAGHGG00-BFFA9FFFFFFFFFFFBF +@M01368:8:000000000-A3GHV:1:1109:8763:7859/2 +GGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG ++ +>AAABFFFFFFFGGGGGGGGGGHHHHHHHCHFAFHHDGEGFHHHHHHHHFHHHHFHHHHHHGHGGHGGHHHFHGHHHHHFFHHHHHHBGHFFHGHGHHHHHGGEGGHHHHHGHHHHHHHHHGFGHHHHGHGHGHHCCGGGGGGGGGGAAGF?FFFFBFA@=BDDFF?-;FFF;@CFFEFEFFFFFFFFFBFDFFFFFFFFFFFFFFFFFFFFFF:FFFF/BF/FFFEFF?DECAFEFFFFFE:FFFFFFFB +@M01368:8:000000000-A3GHV:1:1110:12808:18367/2 +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACAGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATT ++ +ABCCCCDDDFFFGGGGGGGGGGHHHHHHHHHGGGGGGHHHHFHHGHHHHHHHHHHHHHGHHHGGHHHH3GFHEFHHHHHGHHGFHHHHHFGHHHHHGHGHGGHGGGGGGGHHHGGCGGGGHHGGGGGGGGGGGGGGGGGGGF-BAEFEBEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFAFEFDFFFFFFFFFF0BFBED=@DFFFFFFFFFEFFFFFBFAFB;0: +@M01368:8:000000000-A3GHV:1:1110:14751:26540/2 +ATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGGTTGGGCTATTTGGGTTTTTTGACCCTGAAG ++ +BBBBBFBBBBBFGGGGGGGGGGHHHHGGFHGGHGGCHHHHHHGHHHGHHGEGGGHHHHHHHHHHEFHHHHHHGEE?FGHGEHGGHHHGGGGGGEHHGGGGHHGGGEGHHHGHGGGDFGHHGHGGGGGCGAFFCCDFHHHH1CGGHBHFHFCGFFCDFHGCCE.CC:EGFHHCGHHGCF?FGGGFGGG;B9;FFFFFFEGEBF0;;;0;CFBFFF?D.DE.:..99-...;;//9A.;DE.9-./:FB.;// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/2 +GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG ++ +BBCBCFFFFFFFGGGGGGGGGGHHHGHHHFHHBGHHHGGGGHHHHHHGHHHHHHHHHHHHHHHGGHGGHHGHHHGGBGHHHHHHHHHHHHHHHHHGGFHHHGGGEGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGDGGGGGGGGGBFFFFFFFFFFFFFFFFFFFECB-=BFFFFFFFFBB?E-A::FFBFFFFFBFFFFFFFFFFFFBFFEFFF;0BFF0:FE?FFFFBFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1110:16559:7507/2 +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAAT ++ +>AABBCCCCFFFGGGGGGGGGGHHHHHHHHHGGHGGHGHFHHHHFHHHHHHHHHHFHHGHHHHGHHHHHGGEEGHHHHHHHHHHHHHHHHHHHHHHGHGHGHHGGGGGGGHHGGGFGAGFGGGGGGGGGGGDDDFAGGFFFFCFAFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFE..@BFFBD./;:0FFFFF09B/AFCA=-99BFFBFFFFFFFB:BFBFFBFB9: +@M01368:8:000000000-A3GHV:1:1110:16700:6843/2 +GTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTT ++ +CBCCDFFFFFFFGGGGGGGGGGHHGHHHGGHFHHHGGGGGHHHHHHHHHHGHHHHHHHHHHHGGHGGHHHHHHHGBGFFHHHHHHGHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHFHHHHGHCG/GGHHGGGGGGAFGEEADAGGDFFFF00D>CFDDFFFB?AF?B;-@>.FEDFFFFF0BF-BDFFFFE00B0BF0FFFF:BFA0B0:BBFBBFFFFF +@M01368:8:000000000-A3GHV:1:1110:18014:7856/2 +CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTAT ++ +CDDDBFCDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHGHHHHHEGHHHHHEHGHGHHGGGCCGGHGHGCGGGGDHHHHFHGGGGGGGGGGGFGGFGAC-EFEGGGFFFGFF;DFFFBFFFFFFFFFFFFFFFFFFFEFFFBFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1110:23303:11846/2 +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTAAGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAA ++ +BBCBBFFFFFCFGGGGGGGGGGHHHHHHGGHHHHHHHHGH5GHHHGGGGHHHHHFHHHHHHHEHHGFBGEEFE1FG5GFHHHHHFHHHGGGGGHHHHHHHHHHHGGHHHHHGGGGFHHFHH/EHHHGG?@EFHHHGGGGHFGGGGHHFHGGDGGGGFFFHGFDGGGCGACC;DFFB0CH0CCCFGBFBFB/:A?FFFE?AA.CFBECE0BBBF0F/A./9FFFFF./;/FFFFFFA.:////9BB/B/BB/ +@M01368:8:000000000-A3GHV:1:1111:13195:14562/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +ABBBBFBBBBBFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHDGHHHGGGGHHHHHHHHHHHHGHHHHHHHHHGGGGGHHGHHHHGFGFHHHHHHHHGHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHGFHHHHHGFGHGHHGGGGFCGFGFFFFAFFFFFFFFFFA;BADFFFAFFFFFFFFFEFFFEFFFFFFF;FDBFFFFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1111:14287:20817/2 +ATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATGAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGTTAGACCTGTGATCC ++ +CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHGHHHGHHHHGHHHGHGHFHHHGGGGHHHHHHHHBGGGFHHFGGHHGGHGHHHHHHHHEGFFHHFGGGGGHHEHHHBHHHHHFFHHGHGGGGGHFGF3FDGHHGCGGFGHHGGGG/2GG@E?GHHHGFEDGGCFDFFFFFFFFFFFBFFFFFFFFFFF/FFF/BFFFFFFFBA.?@;FFBDFFFF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/2 +ACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGT ++ +BBBBBFFBABBBGGGGGGGGFGHHHHHHHHHHHHHGHHHGFHHHHGGGGDHHHHHHHHGFHHHHHGHHHHHHGHFHGHHGGGDFGDFFGGGFFGFFGHGHHHGGC?AD-:A-AFFGGG-?9EFEFGGFFBFEFCFFFFFFFBBBFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFEFFFFFFBFFFFEFEFFFF;CF-FFFFFFFF/BFFFFFFF +@M01368:8:000000000-A3GHV:1:1111:8665:25542/2 +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGACAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTA ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHCHHGDGGGGHGGHHHHHHHHGHGHHHGGGGGHFHHHHFHHHFFHHHHHFGCGGEHFHHFGGHFHGGGGGGHHFEEEAFEFFDFHGHHHHGGGGGGGHH0DGGGGCGHCC-FFFFFFFGGGGGGGGGGHHHHHGHHHHGHHGGHHGGHGGHHHGHHHHFHHGHHAFGGGHHHHHGHHHHFHFHHHHHECGGGHGHHHEFHFHGGGGGGGGFGFFGFFEFGEGHHHGHHGGDGGGHGFGGGGGGGGE@GCGGHHHGHHHHHGHHHHFHHGEGFFEGCE.ECCECEHCGGFFE/AABFFG0CFE0BFFF9CFGG.F/BBBFFGFGGGFFFFFFBFEDAEFFFFFBFFFFFFF0;FEBF: +@M01368:8:000000000-A3GHV:1:1112:10272:7828/2 +GTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC ++ +BBCCBFFCCCCCGGGGGGGGGGGGGGHHHHHHGGGGGGHHFHGGGGGFGHGGGGGGHHHHHHHHHHFHHHHFHGFFHHGF?ECEFFFFFFHHHHHH?FHHHHHHHHHGFHHHHHHGGGFGHHHHFHHHHHHHHHHGGGFGFGCGGGGHHHHHHHHHHHGGFFHGHHHHHFFHFCGFHCCGHGHCGGHG?DGG +@M01368:8:000000000-A3GHV:1:1112:9832:16531/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBBFBBBBBFGGGGGGGGGGHFHHHHHHHHHHHHHHGHHHHGHFHHHGEEGGHHHGHHHHHHHHHHHHEHGHHGGGHGGHGHHHHHGHHHHGHHHHHHHHHHHHHHGHHHHHGEGCGHHHHHGHHHHHHHHHHHHHHGHFFGHGHHGGGDACDFFFFABFFFFFFFFFFD-BC?DA9.DFFBEA==B=?F.;ABBFBFEF-DAF/BFF9/FFFBB/9BFFFFFFF/BFBBFFFFFFF/9FEA?--B/;. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/2 +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATT ++ +BBBBAFFFFFFFGGGGGGGGGGFGHHHHHGHHHHHHHHHHHHCGHHHHHHHGHHHHHHDGHHGGAECHHGHHHHHHHGHHHGHGFHHHHGGHGGHHFHHHHHHFHHHHHHHHH2GHHHHGHGHHFHHGGFGGGHHGHHHHHFHHHHEFHHHHEFGFFHGEHCFGDFDFFFFFCFFFFFFFFFFFFFAFBFFDFFFFFFFFADCF?9?EFBFB9EF-A.;BFFFFFFFBFFFFFFFFFFFFBFFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1113:13532:8618/2 +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTGGAT ++ +CDDDBFFFFFFFGGGGGGGGGGHHHHHGGHHHGHHHGHHGGGGEHHGGHHHHHHHHHHHHHHGHHGHHHHHGGHHHHHFHHHHGCDCGHHHHHHHHEHHHGHGHHHGFHGGHGGHHHHHHHHFHHHFHHHGHHHHHHHHHFGGHHHHGGGEGAFHHGHHGGHHHHGHFBGFHGHGHGHGGHGGF@DAFEFBECAB=A.0BFFFEDF=A9.@D.-AAFFFA-:-..:.9/0:;0..-..0000::BFB09:: +@M01368:8:000000000-A3GHV:1:1113:21679:18011/2 +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +BCCCBFFFFFFFGGGGGGGGGGHHHHHFHHHGHHHGFGHGGHGGHHHHHHGHHHHHHHGGGGFHHHHHHEGHHHHHHHHFGGFCGEHFHFGEGHHHFGGGGGHHHGGGEHGGGGGHHHHHHGDCCCGHHHHDGGGGCD/FCC->DFFF. +@M01368:8:000000000-A3GHV:1:1113:5741:16959/2 +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF. +@M01368:8:000000000-A3GHV:1:1114:10130:11959/2 +ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACG ++ +BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGHHGHGAGAE +@M01368:8:000000000-A3GHV:1:1114:14540:5315/2 +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC ++ +CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/2 +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A.... +@M01368:8:000000000-A3GHV:1:1114:16639:15258/2 +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG ++ +CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0 +@M01368:8:000000000-A3GHV:1:1114:2404:13066/2 +ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGA ++ +CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFF diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_1.fq b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_1.fq new file mode 100644 index 000000000..43f9744f2 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_1.fq @@ -0,0 +1,388 @@ +@M01368:8:000000000-A3GHV:1:1101:14518:9998/1:GTTATTAT +TATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT ++ +FFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A// +@M01368:8:000000000-A3GHV:1:1101:18422:19051/1:GTATCCGA +CATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +DDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF. +@M01368:8:000000000-A3GHV:1:1101:25545:21098/1:ATTAATTA +ACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG ++ +5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/A@FFFGHHHHFHEFGDABFFGG/@DCE;>=EF?AEFFFF;9;=DAFFFFBBFFFBFFF//;BFB.:FBFFBB/BFFFF/BFFE?EFAFEF9 +@M01368:8:000000000-A3GHV:1:1104:11928:24197/1:ACGTAGGT +GCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATA ++ +FFBCGGGGGGGGGGHHHGHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHGGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHGHHHHGHHGHHHHGGHGEEGGGGFHHFHHHGHGEHHHHHHHHHHHHHHHHHGGGGGGFGGGGGGGGFFGGGFGFGAEFEFGFEAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@D9 +@M01368:8:000000000-A3GHV:1:1104:12288:20635/1:CACTTGGG +GGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGCCGCAGCATCTGTCTTTGATTCCTGCCT ++ +B2>AFGGGGFFGD5GGHGFFHGHEGGGGHHHHFFHH5FHGHHHFFHEFHHHHHHGGHHHHHGFHGGHGGGGFHGGGFBHHHFGEGHHHHGHGGGGECEHHFHHGHHFFHFGGGHHHEGHDGHHGHGHFHHHECGCBCHHGFHHFHD1GFHEFHEF?GDCFFEFE0A@;@>BD/9BFBBBBFDFFFF99D=?>DDBFF-AFFEBB9BBEFEFAFFF//-@---;;FBBFBFB///;99999BA9 +@M01368:8:000000000-A3GHV:1:1104:13832:4398/1:CACGATGG +ATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTC ++ +FFFFGGGGGGGGGGHFHHHHHHHHHGFFHHGGHGGGGGHHHHHHHHHHFHHHHGHHHHHGGHGHGGHGGGGGGGHGFFGGGGDGGHHHHGGGGFGGGGGCFGGEGCDGGGGGGGGGGGGEGF?;BFFFFFF +@M01368:8:000000000-A3GHV:1:1104:23670:4161/1:ATTCAATT +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCC ++ +FFFFGGGGGGGCGBBGGHHHHHHHHHGHHHHHHHHHHFGGHHHHHHGGFHHHHHHHGGGGGFHHHGHHHHHGHHHHGHHGGGHGGGGHHHHHGHHHHHHEGGGFHHHGFFDGEGHGHFHGHHGEGGGHHBGHGGHGHGGGGG/@FCDFDGFHGGGDFFHFGFFGGGGGHHHHGGGGGGGEGCDG?GGBFFFEE00BFFGABBBAFGGGEGEA.9FFF/./;BFBF./AAF/BFFBBF/F/BFB +@M01368:8:000000000-A3GHV:1:1104:24927:22253/1:AGCTAAAG +TGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTAT ++ +3DFFFGGBGFF3EAEEEHFHHFHHHGHHHHDGHHGAEFGHHHGFCHHGHHHBGHHHAEGGHGGFHFBFHHHHHHHHHHFHH1EEHEEHH1FFDEEFCGHBGHHFHEHHHHHH1FCGHHHHEEFGEEGFFCHHH11>GHHF/FG2DGGCGAGGHGGGG@@@BEFFF?@@@FFEFFFFFF?@@FB@BB@FFFE=;==---A9EFBBB/;E;A9B/B/FFFEF/B///;/;9/A/;/9BFFFBFBB +@M01368:8:000000000-A3GHV:1:1104:4705:7727/1:CTACAAGC +ATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +FFFFGGGGGGGGGGHHHGHHHGHHHHH6GHHHHFFGGGHHHHHHHHHHHHHHHGGFGGGEGGGHHHHHHHHHHGHE3FGGGGHHHHHFHHHHHHHHHHHHGGGGGHHFHFCGFHHGGGGGGGHHGGGGHHGGGGGGHHHHGGGADCHHHHGDGGGGGGGGC@DGFHEHHHHHHGHHHHGFGDEGFGFFGGGGCFGBEGFGGGFG;C.BFFFFFFFBFBFFFF/F?.AFFF/BFFEFFFFFEFF +@M01368:8:000000000-A3GHV:1:1104:7756:4776/1:GGCCCATA +ACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +FFFFGGGGGGGEEFHHHHGHGHHHHHHGGHHHGGGGGGHHGHHHHHGHHGHHHGGFHHHHHHHHGHHHFHHGHHGFGGGGHHHHHHHHGHGHFFHFHHHHHHGGHGFGFHHHGHG?FGHHHHHHHHHHHHHHGHGHHGHGGCDGFFHHHHGHHHHHGHHHGFHGHFHGHGHGH/@CABFFFFFFFACAFF?BBFFBFD-@-.D>FFAF.F.:9---;AADFFFFFBEFFF:9FFFFBBFFFF/ +@M01368:8:000000000-A3GHV:1:1105:11310:21761/1:ATAAATAA +TAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTT ++ +FFFFGGGGGGGGGGGHHHHHHHHHHHHGHHHHHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHGHHHGHHHGHGHHGHHHHGGHGGG=FFGEHHHHHGHFGGHHGHHHHHFHHHHHHHGGHHHHHHHGHEHHGHHHHHGGGGF9AGE?DEGFFGGGGGGGGGGGGGGFFFF/9FFBFFFFFFFEFFFBFFFFFFFFFFFFEFFF0 +@M01368:8:000000000-A3GHV:1:1105:11578:14676/1:ATTGAACG +TAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTC ++ +BFFCGGGGGGGGGGHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHFGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHHHHHHHHHGHHHHGGGGGGHGGHGHHHHHHH;CHHHHHHHHHHHHHHHGHGGGGFGGGFGGGGGGGGGGGGFGGGEGGFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1105:13575:19255/1:TTAGTAAG +TATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGTTCCCGTGAGTGGTTAATAGGGTGATAGGCCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG ++ +FFFBGG3A111FFAEGDDBGFDHF00F01BBA00BFGEHFBFFA1FABB0FAE?CFHF1BGFHFB0011F121E//>>1F10>B?EFHGCC/?/BFG/EEGFFEE//BCFDE0?E@@B/?11;B=.9.;.BBFFF..;A;/B/;B//;;//BBF/ +@M01368:8:000000000-A3GHV:1:1106:22927:3863/1:GTATCCGA +CATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGACTT ++ +D@AFGGGGFGGGFGFHHHFFH4BCBGHHHHGFFF3G5BF3322EEAFHHHHHHAB5GHFHEHFHHH3BEEHFGF5@13FDF3GDGFHHFGHHHGHHHGFGGHHFCG//?/EGHHHG3F4BFFGHHHEDGFHHB/B/?FBF<@-9?BDEFFF?B--?DFFFB9FA>B;A.BFDB?AB.--@;-.FFAEFFFF9AE;DDFFFFB/9BF +@M01368:8:000000000-A3GHV:1:1106:23625:4236/1:TAGCTAAA +GTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTA ++ +FBFFFGGFGFGGGEFCGGHHHHFGHGHFHGHHHHGGFGGFGHHGHGHHHHGHGFFHHGGGGGHHHHHHHHHBFHHEFHHHHHHGF?FAGHGFHHHGDGFHHGGGHGHFHHHGHHHGHHFHHGFFGFHHHGHHHHFFHHHHH/FGHHHHGHGHGBFFF9 +@M01368:8:000000000-A3GHV:1:1107:14451:26748/1:GTATGTTC +GCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +ABBBGGGGGGGGGGHGHHHHGAGHGGGGGHHHHHHHHGHHHHHGGGGGGFFHHHHHHHHHFHHHHHGGGGCHFHH3FEHHGCGGGDGHHHGFGGHHGGGGHHHHHHG/DGGGHHHHGGGGGCCHGG?CGG1GHHGHHHHBGHHHFHHGHHHHGGADAD00ECEGHEFHHFFAEFFFFFGGFBFBFFFGFFG.;B/99;BCFGGGGEFFFFFFEDA./:ADEB?FBFFFF;FFEBFBFFB./9. +@M01368:8:000000000-A3GHV:1:1107:18714:24788/1:GTATGTTC +GCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +DEDEGGGGGGGGGGHHHHHHGGHHGGHGGHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHCFGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHGHHHHHHHHHHHGHHHHGGEGEGCCEGGHHHHHHG:CAFFGGGGGGBFEFGGGGHGAFFGGFGGGGGGGEFFFFFFFFFEF/EDDFFFFFFFFFBFFFFFBBFFBBF/ +@M01368:8:000000000-A3GHV:1:1107:21355:8333/1:ATATTGAA +CGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +FFAFGGGGGGGGGGHHHHHHHHFHHHHHGGGGGHHHHHHFHHHGHHHHHHHGGGGGHHHHFFGHGHGGGGGGGHGGEGGGHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHGHHHFHHHHHHHHGHFFHHHHGGHGEGHHGHGFHHFHGHCEFHEGHGHHHGHHHGGGGGGCFFFFBFGGFGGGGFBG?FDGGGEGFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF.AA/9 +@M01368:8:000000000-A3GHV:1:1107:22864:15712/1:AATAAGAC +ATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTAC ++ +FFFFGGGGCEGGGGHGHHDGFHHHHHHHHHHHHHCHHGHFGBGDFGE?GHHGHFBHHFHHHHHHHHHGHFGFGHGHHGGC@DCFGHHGGGGGGGHHHHHHGGGGGFGGGGFFGGGGFADGFEFFFFFFFFFFF9;FFFF/BFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFEAECDFFFFFFFFFBFFFFF +@M01368:8:000000000-A3GHV:1:1107:24817:14233/1:CTTCAGGG +TCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACAT ++ +BFFFGCFGGGGGGGHHHFGCFGGGFFGHHCGHHHGHGHGHBFFHHHEDGGFGFGHHFFFHGGEGHFHHGHFHGFFHHHFGHHHFHACECEHHHBGFHGFHHHFHHF4GFHFHFHEHGGE/EG:A-CFGGFGADGGGGFGGGGDAAAADFA.-AFFECFDAAFFFFEFFFFBFF;D;BFFFB/;BFFFFFFFFFFFFFFBFFBF/;//;BFFFF?FFFFFFEDAFFFFFBF//:BFBACF--9/ +@M01368:8:000000000-A3GHV:1:1107:24830:14440/1:AACTGTAT +CCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +FFBBGGGGGGGGGGHGHHGHHGHHHGGHHHHHGHGHHGDHHHHHHAGGGGFHHGHHHHHHGHHHHHHHHHHHEGAFGFHFHHHHGEGHHHHHHHHHHHHHHHHHGGHHHGEFEGGHHGHHHHHGGHGFHH/?GHHHHGFGHGFHCGGBBDAFFFEFFFFFFFFFFFFFF=CDDADDFFFFEF=BFFFEFFFBFFFFEEBF./:FFFFFFFFFFFFFFFFFFFEFFFFFFFFFFF/BFBEFFC- +@M01368:8:000000000-A3GHV:1:1107:26478:23602/1:GCTAAAGT +GAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGAT ++ +13BBBEGGGFGGGGGGHHDB1BGFHHHFGFGGG0F00BGBGFGGF1GBGB1BGCGAEE/FGFHGHFHHHHHBFF1B0FGGF//F//FGFGFFF/1@B1DFHHHGGEFEDHFDFAFF0B//1FDD1GFFHHDF?1BD>GF/GCAC0C@?@-;99BBB->@--;-B//99B--9-BF=A--A-:A----9AA9AFBFBBB?E@BBFFFFFFFBFFFFF +@M01368:8:000000000-A3GHV:1:1108:11059:23181/1:GTTATTAT +TATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGAT ++ +FFFFGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGHIIIHHHHHHHGHHHHGHHHGGHGGHHHHHHHHHHHHHHGGGGGHHGHHHHHHHHHHHHHHHGGGGGHHHHHFGHHHGGGGGGHHHGGGGGHGGGGHHHHHHGGGGGGHGGHEFGGGGGHGGG-ECHHHGGGGGGGGGFGFFGGGGFGGGCF?EFGG0;BFFFFB?9AAFFFFFFBF;BBFFBFFFFE?F/ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/1:TAGGTGCG +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +CCCCGGGGGGGGGGHHHHGGGGGHHHHHHGHGHBGFHHHHHGGGGGHHGGBFGHHGGGGGGGHHHGGGGHHGGGFHHHHHHGGGGGGHGHHGGGGGGGGGGGGGGHHHHFHHHGHGHHHHHHGHGHHGGFGGGDFFGGHHHGHGH/FHHHFHGHGHHGHHHGHHBACFHHGDFGGGGGEFGC?EGHHHB0CGHHGCGHHHHBEHGHH.::ACA;FECFGGGGGFFFEFGGGGGGGFFBBBFGBFFFEFFFFBFFFFFFBBFBFFB9..AF?FFFFF +@M01368:8:000000000-A3GHV:1:1110:14751:26540/1:TAACACTT +GGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACTGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGTTGTGCACGCGATAGCATTGCGCGACGCTGGCGCCGGCGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG ++ +FFADGEEGFGB1112DGDGHGFGHHCG/ECEBGGHDFGHHFHGHEB1BCGFFE2EGHHGHFFFHHBFFHEFCGGHHFHHHHH111BFFHGHEHBEHGGECEFHGFHFGGDBBGHHBHHHH0GH22FGHGFFFH1BFCG0F@FGG11@GDHFG1D/1FGFHH/FCG.>0><-<@CCFFG.CC-@C?C9FFF0C---;------;9----9-9@-AAFF9B9---9-/;B9BF/9BB//B/;/// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/1:CTGTAATA +TTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +FFFFGGGGGGCBGGE?GGGHHHHHGHHBEGGHHGGGGGHHHHHHHHHHHGGHHHHGFGGGGHGHGCFGHHHGGGCGGHGHGGGGGHFGGGHHHHHHGCEFGGHHHHGGGGGGGHGG/CEGHHHHGFHHHGFHHGFFHGHGHFGGEGFDDGGBCGHHGFHH/CHHHHGHGHF0CFGGGGGGGFFFFFBFFFFFFGFFGGF?DGEDEEFEFFFF?FFFFFFFFFFFFFFFBFFF.BFFFBFBBA; +@M01368:8:000000000-A3GHV:1:1110:16559:7507/1:CATTCAAT +TGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAACTGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +FFFFFGGGGGGGFGGGGAGHHGCHHGHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHFGGGHHHHHHHHBDHHHHHGGHFEEGHGGHHHHHHHGHHHEHFGGGGGGHHHF33FGHHG3GDDGH//EEGHHFFBF?GHHFCC@DGFCGGB?DGHAFGGHHGFH0E??<@DGHGGCFGGF?DGGGFFGGGGGGGG.C/0BBF?FBBEGG0FFF.AA9;B9/E////99;;:.//:FFFFBBF//9 +@M01368:8:000000000-A3GHV:1:1110:16700:6843/1:AAATAATA +GGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAAC ++ +FFFFGGGGGGGGGGHHHHGHHHHHHHHHHHHGGGGGHHHHHGGHGHGGGGGGHHHGFFGHHGGGGHHHHHHCGG@FGHFHFEGGGGGGHGGGGDGHHHHHHHHHHHHHHGHHGHGHHGGGGGCGHEHGHHHFHHHFF.DGHHHHHHGHHHHHHGFGHGCGHGHHHHHHHHGHHHCD?:A::FCDGEGFGFFBFGBFGGGF00CBFFFF/BFBFFFFA +@M01368:8:000000000-A3GHV:1:1110:18014:7856/1:ATAAATAA +TAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG ++ +FFFFCGGGCGGGGGGHHHHHGFHHHHHHGHHHGGGGGFHHGHFGGHHHGGFGGGHHGGGGGHHGGGGHGGHHHGGGGGGHHGHGDGGGGGGGGB/ACC=@--AFBFFB?=BFDFFF//FDB;-9A-AD-.A.A=?-9-:B/AEB/BFF.A;DDFFFBBFFFF/BBFFFFBFF9B; +@M01368:8:000000000-A3GHV:1:1111:13195:14562/1:ATCAAAGA +CAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATAC ++ +FFFFGGGGGGGGGGGHHGG4FDFGFGGCGGGHGHG?EGHEGFFDHFHHHHGGFE@EHHGEEEGFCCEFFGFG/EHHHHHBFBGGHFHFHEHGHEFGGGED/EFDEFFEHHBGHHCFFFDFGGHHGFFFHHHHGFG>0<0DGGFHBGHFBDFGHGFFGGAGHHGCGBHFFHHHFFFBFGGGGF/:FFFCB9F9FF0FEFE?FF0BED-D./ +@M01368:8:000000000-A3GHV:1:1111:14287:20817/1:GCCAACAC +GTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTCATCGCACCTACGTTCACTATTACAGGCGAACATACTTATTAAAGTGTGTTAATTAAT ++ +ACFFFGFGFGGGGGHGHHHHHHHGGGGGHGHFFCGHHGBGHFHHHHAGHHHHEHHAGFFEHEAE?GHHHHEGFFFDGHGHBFFHFHHHGHGHGHBECG@@@EHGGEGCGGGGFFGGGG?BGGGGGG.-C.FEDCFFFEFFFAF/99BEFA.:9BFB/9FFFEFFFFFFEFFF/FBBFFFFFFFFFFFB//;.@@//;DFFFF//BBFFFBF;A;DF=>B//;9B//B/;/;9//9//;B/:B9 +@M01368:8:000000000-A3GHV:1:1111:23624:14516/1:GTCCTACA +AGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGGGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAG ++ +FFAFGGGGGGGGBGHHHHHHGGHGGHEHGHADFHHHHEGGGHBGHFFHHEHHGHFHGG5FBEEGEGHHHGHHHEFDGHHFFGFGGHHGHHHGHBHGHFHFHHGGGGFCFBGFGE?GFBECEGDGHEHGDGCGHGC/DF@GHGFFCGGGGFFFFDD?@C@GFEC?-ADHFFHBGHFBHFG0CC//.;B0/CA.;AA.;@.AB/9BB/A/.AFFFE/BFFF///9B/FBDE9/;99/B/BFFEF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/1:ACACACTT +TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGT ++ +FFFFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGFFEHGGHHHHHHHHHHHGHHGGGGGHHHHHHFHHHHGHHHHGHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGCGHHHHGHHGHHHHHHHEDHHGHGGGGGD;BEGGGFFGGGGC:CFGGGGGGGGGFGGGFFFGFFFFF; +@M01368:8:000000000-A3GHV:1:1111:8665:25542/1:TCCTACTT +CAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTGTCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +FFFFGGGFGFFGGGGHGH4AGGGFHHCGEE2FGHHHHHHHHHHGFHGF53FHEGGFAF5CFHHGGFGHFHHGGHHHCHHHHHHHFHHGH?EEEG1FFFEHHFHFGGHHGG?F4FBGHGHCHEF0//-9--;0CFGG?@BGDGFFFFEFBBBDA?FFBFFFF=B;-9.AA9EFFFF/;9BD.//;9/9/B:/:BFBFFBFFF/B:BFF//;/B/FFFBFF.A-BFFFBA/F//BFFFBF/;/A- +@M01368:8:000000000-A3GHV:1:1111:9655:13916/1:GGCCCATA +ACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +FFFBGGFE1EEEEGGHGHHH2FGHHHFGFGHGCFGGGEFHGGEGGHHHHGHEFBFEGHHHGHHBEHHHHGHGFHHHGGGGHHEGGGGHHHGFHGHHHH1FHHG?G/AGF1GBFGEFFHF2FDD0FG--99@=---AAABA-BF/B?A@F-9BBFF//BB/9/ +@M01368:8:000000000-A3GHV:1:1112:10272:7828/1:GTATCCGA +CATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAC ++ +BBBFGGGGGGGGGGHGHHGHGHHHHHHHHHGHHHGGHDGHHHGGGGHHHHHHHHHHHHHHHFHGHHHHGGHGGHHHFHHHHHCGHFFHHHHHHHHHHHHHGHGEFGAEEEEHHGHHGHGHHHHHHHGHHHHHHGHGHFFBC/BA?BGGGFFFFFFFFFFFFFFFC-@DDFFFFFFFEFAFFFFF +@M01368:8:000000000-A3GHV:1:1112:9832:16531/1:CTGTAATA +TTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC ++ +FFFFF4GGGGEBGEFGHGGHGHGHHHGGHFBGFGGGGGHHEFHGEHFHFHEHHHHHGCGGGHFHHCFGHE@1EEEFFGB?EEEEHBGGGCHHGHHBEE@>EAHHFAEBDGGGCEFF?CEGFFHHHHHFHHHFHGHCGCAHHF<..C.D=0CD.GFHHHG.CAGHC:CHB0GGGFFB0:CFA.A-;9.;000CBBFFBFGA.9AA;A;EDDE.ABBFFFF9;BEFFF/BF//9/B//9:B//.. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/1:CGCCTGTA +ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA ++ +FFFFGGGFGGGGGGHHHGGHGGHHHHHHHHHHHGHHGGGGGHHHHHHHHHHHHHHHHHHGGCGDHHHHFGGHHHGGGGGFGGHGGGGHHGGGGHHHHHHGGGGGGHHGGGGDGGFGHGGFCDCHHHHGHHHHGHHFAGFGGEHFGEG.C/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/; +@M01368:8:000000000-A3GHV:1:1114:2404:13066/1:TCCTACAA +GCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT ++ +FCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFFBFFFFFFF diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_2.fq b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_2.fq new file mode 100644 index 000000000..545b523f0 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read1_2.fq @@ -0,0 +1,388 @@ +@M01368:8:000000000-A3GHV:1:1101:14518:9998/2:GTTATTAT +CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACAT ++ +CCCCCFCCCCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/: +@M01368:8:000000000-A3GHV:1:1101:18422:19051/2:GTATCCGA +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +BCCCCFFCFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF +@M01368:8:000000000-A3GHV:1:1101:25545:21098/2:ATTAATTA +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT ++ +3AAA34BFFFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<.<<AABBFFCFFFGGGFGGGGGGGGHHHHHHHHHHHHHHHHHHGHHHGGEGGFFHHHHHHGHGHGHHHHHEHFHGHHHHEFHHGHGGGGGHHHHGHHHHHHHHHGFGHHHHHGHGHGHHGGGCCGGGGFGGGGGGDGGGGFGDGGGFFFFFFEFFFFFFFBAF:9AF//;BEF-DD/FFFFBFFFFFFFFFEBFF?FB;/;//BFFEFFE/::..9;-:B9: +@M01368:8:000000000-A3GHV:1:1102:17584:10050/2:ATCAAAGA +GTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG ++ +ABCCCFFFFFCFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHFHGGHGGHHHHHHHHHHHHHHGHHHGGHHHHHHHGGHHHHGGGGGHHHHHHHHHHHHHHGGHHHHHHGHGHGGHGGFGGGGGGGGGGFGGFGGGGGGGGGFFFFFFFFFFEFFCFAAFEFEFFFFFFFCFDFFFFF +@M01368:8:000000000-A3GHV:1:1102:18842:24844/2:CACTTGGG +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +CCCCBFFBFFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHFHHHHHGHGHHHGGHGGHHHHGHHHHHHGHHGGGGGHFHHHFGHHHHHHHHHHHGGGGGHHHGFECGGHGGGGGGHHHGGGGHHGGGGHHHHHEFDCADGHHHHGGGGFC?AE-@DDFHFFHHHCFHGGFFGFFFGGGEFEGFGED9C?CEGF90FEF/A./BBF9FFFFFFFFBFFF.9AF////;FFBFFB/:BF +@M01368:8:000000000-A3GHV:1:1102:21788:11027/2:GCCCACAC +AATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAAC ++ +CDDDDFFFFDDFGGGGGGGGGGHHHHHGGGGHHHHHHHHGHHHHHHHGGHHGEHGGHHHHHHHHHHHHHHGGGGEHHHHHHHHHHFFFFFHHHGGGGGHFHGBFEHHHGGGGGGGHHGGGGHGGGGGHHFHHHGGG@CGHHHGGGGGGGGGGGEGDGFFDHHGEHHBCFHGBGFAGGHFGGCEEF0BE///FDFACF?FHFGC//??1B0<FF>DFCFDFFFFFFFFF-BBAFFFFFFFFE@D9B +@M01368:8:000000000-A3GHV:1:1103:25465:20010/2:GACATAGG +AACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCAC ++ +AAABBFFFFFDFGGGGGGGGGGHHHHHHGHHHGFHHHHHHHGGGGGHHHHHGHHHHHHHHEHHHHHGHGGHHGGGHHHHGGGGGHHHHHEHFGEHHHEE14BGHHHGHGHFCE/EFGGGGGGHGGGGGG?FFGGGG.ADGGGFFDA.FFEC--;9BB +@M01368:8:000000000-A3GHV:1:1103:25519:6301/2:AAATAAGA +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATGCTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGATG ++ +>AABBFFFFFFFFFFGGGCAFGCGHGGGHGGGHHFHHHFHHGGGGGFFFHHHBHHHHG5BG5GFEEEE1FGFFGF1EGHGGG/BFHEF@EA1BE1@EED3?4DHGGGGEGHFFFDDG?DCDEG@<?@DGCAGC-;@DGFFHGCHEEFGGFGFB/;..BBB.CCE?A0FE0EBFF0FEF.;=DFFB//BFBF//;/:9BA.9FB9//;9//;9F;FF +@M01368:8:000000000-A3GHV:1:1104:13832:4398/2:CACGATGG +GACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGAT ++ +BBCCCFFFFFFFGGGGGGGGGGGGGHGGGGGGGHHHGFGGHHFGGGHGHHGHGFGECGHHHHGGGGGGGHEGFGGGHHGHFHHHHFGHFHHHHGHHHHFGGFGG3FFGGHHHHHHH2?FFGHFHHHHHHHH +@M01368:8:000000000-A3GHV:1:1104:23670:4161/2:ATTCAATT +CGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAA ++ +A3AABBFFFFFFGGGGGGGGGGHHFHHHHHHGHGHHHHHGCHHHHGGGGHHHHHHHHHHHHHHHGHHGHGHGGHGGHGHGGHHGFGHHGHHHEHHGHHHHHGHEHEHHHGGFGGHHHFHHHGHHHHHHHGHHHHG4EGGGFCBBCA?DGGGGGGCCAFFFFFFFFFFFFFFFFFDFFF.9@--=AFFFF;FBFFBEFFF9FBFFB9/FFFFFFB/FFFFFFFBFFFF/BBFBB/FFFE?.;@FFB?FBB// +@M01368:8:000000000-A3GHV:1:1104:24927:22253/2:AGCTAAAG +GTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGGGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACGAG ++ 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+GGTTCCTACTTCAGGGTCATAAAGCCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAG ++ +>AAABFFFFFFFGGGGGGGGGGHHHHHHHCHFAFHHDGEGFHHHHHHHHFHHHHFHHHHHHGHGGHGGHHHFHGHHHHHFFHHHHHHBGHFFHGHGHHHHHGGEGGHHHHHGHHHHHHHHHGFGHHHHGHGHGHHCCGGGGGGGGGGAAGF?FFFFBFA@=BDDFF?-;FFF;@CFFEFEFFFFFFFFFBFDFFFFFFFFFFFFFFFFFFFFFF:FFFF/BF/FFFEFF?DECAFEFFFFFE:FFFFFFFB +@M01368:8:000000000-A3GHV:1:1110:12808:18367/2:AATTAACA +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACAGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTG ++ +ABCCCCDDDFFFGGGGGGGGGGHHHHHHHHHGGGGGGHHHHFHHGHHHHHHHHHHHHHGHHHGGHHHH3GFHEFHHHHHGHHGFHHHHHFGHHHHHGHGHGGHGGGGGGGHHHGGCGGGGHHGGGGGGGGGGGGGGGGGGGF-BAEFEBEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFFAFEFDFFFFFFFFFF0BFBED=@DFFFFFFFFFEFFFFF +@M01368:8:000000000-A3GHV:1:1110:14751:26540/2:TAACACTT +ATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGGTTGGGCTATTTGGGTTTTTTGACCCTGAAG ++ +BBBBBFBBBBBFGGGGGGGGGGHHHHGGFHGGHGGCHHHHHHGHHHGHHGEGGGHHHHHHHHHHEFHHHHHHGEE?FGHGEHGGHHHGGGGGGEHHGGGGHHGGGEGHHHGHGGGDFGHHGHGGGGGCGAFFCCDFHHHH1CGGHBHFHFCGFFCDFHGCCE.CC:EGFHHCGHHGCF?FGGGFGGG;B9;FFFFFFEGEBF0;;;0;CFBFFF?D.DE.:..99-...;;//9A.;DE.9-./:FB.;// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/2:CTGTAATA +GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAA ++ +BBCBCFFFFFFFGGGGGGGGGGHHHGHHHFHHBGHHHGGGGHHHHHHGHHHHHHHHHHHHHHHGGHGGHHGHHHGGBGHHHHHHHHHHHHHHHHHGGFHHHGGGEGHHHHHHHHHHHHHHHGHHHHHHGHGHGHHGGGGGGDGGGGGGGGGBFFFFFFFFFFFFFFFFFFFECB-=BFFFFFFFFBB?E-A::FFBFFFFFBFFFFFFFFFFFFBFFEFFF;0BFF0:FE?FFFFBFFFFFFF +@M01368:8:000000000-A3GHV:1:1110:16559:7507/2:CATTCAAT +GCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAAT ++ +>AABBCCCCFFFGGGGGGGGGGHHHHHHHHHGGHGGHGHFHHHHFHHHHHHHHHHFHHGHHHHGHHHHHGGEEGHHHHHHHHHHHHHHHHHHHHHHGHGHGHHGGGGGGGHHGGGFGAGFGGGGGGGGGGGDDDFAGGFFFFCFAFEEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFFFFFFFFFFFFFFE..@BFFBD./;:0FFFFF09B/AFCA=-99BFFBFFFFFFFB:BFBFFBFB9: +@M01368:8:000000000-A3GHV:1:1110:16700:6843/2:AAATAATA +GTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCC ++ +CBCCDFFFFFFFGGGGGGGGGGHHGHHHGGHFHHHGGGGGHHHHHHHHHHGHHHHHHHHHHHGGHGGHHHHHHHGBGFFHHHHHHGHHHHHHHHGHHHHHGGGGGHHHHHHHHHHHHHHHFHHHHGHCG/GGHHGGGGGGAFGEEADAGGDFFFF00D>CFDDFFFB?AF?B;-@>.FEDFFFFF0BF-BDFFFFE00B0BF0FFFF:BFA0B0:BB +@M01368:8:000000000-A3GHV:1:1110:18014:7856/2:ATAAATAA +CATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTA ++ +CDDDBFCDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHGGGGGHHHHHHHHHGHHHHHEGHHHHHEHGHGHHGGGCCGGHGHGCGGGGDHHHHFHGGGGGGGGGGGFGGFGAC-EFEGGGFFFGFF;DFFFBFFFFFFFFFFFFFFFFFFFEFFFBF +@M01368:8:000000000-A3GHV:1:1110:23303:11846/2:ACTTGGGG +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTAAGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAA ++ +BBCBBFFFFFCFGGGGGGGGGGHHHHHHGGHHHHHHHHGH5GHHHGGGGHHHHHFHHHHHHHEHHGFBGEEFE1FG5GFHHHHHFHHHGGGGGHHHHHHHHHHHGGHHHHHGGGGFHHFHH/EHHHGG?@EFHHHGGGGHFGGGGHHFHGGDGGGGFFFHGFDGGGCGACC;DFFB0CH0CCCFGBFBFB/:A?FFFE?AA.CFBECE0BBBF0F/A./9FFFFF./;/FFFFFFA.:////9BB/B/BB/ +@M01368:8:000000000-A3GHV:1:1111:13195:14562/2:ATCAAAGA +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG ++ +ABBBBFBBBBBFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHDGHHHGGGGHHHHHHHHHHHHGHHHHHHHHHGGGGGHHGHHHHGFGFHHHHHHHHGHHHHHHHGHHHHHGGGGGHHHHGHHHHHHHHHHGFHHHHHGFGHGHHGGGGFCGFGFFFFAFFFFFFFFFFA;BADFFFAFFFFFFFFFEFFFEFFFFFFF;FDBFFFF +@M01368:8:000000000-A3GHV:1:1111:14287:20817/2:GCCAACAC +ATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATGAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGTTAGACCTGTGATCC ++ +CCCCBFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHGHHHGHHHHGHHHGHGHFHHHGGGGHHHHHHHHBGGGFHHFGGHHGGHGHHHHHHHHEGFFHHFGGGGGHHEHHHBHHHHHFFHHGHGGGGGHFGF3FDGHHGCGGFGHHGGGG/2GG@E?GHHHGFEDGGCFDFFFFFFFFFFFBFFFFFFFFFFF/FFF/BFFFFFFFBA.?@;FFBDFFFF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/2:ACACACTT +ACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTA ++ +BBBBBFFBABBBGGGGGGGGFGHHHHHHHHHHHHHGHHHGFHHHHGGGGDHHHHHHHHGFHHHHHGHHHHHHGHFHGHHGGGDFGDFFGGGFFGFFGHGHHHGGC?AD-:A-AFFGGG-?9EFEFGGFFBFEFCFFFFFFFBBBFFFFFFFFFFFFFFFBBFFFFFFFFFFFFFFFFFFEFFFFFFBFFFFEFEFFFF;CF-FFFFFFFF/ +@M01368:8:000000000-A3GHV:1:1111:8665:25542/2:TCCTACTT +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGACAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTA ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHCHHGDGGGGHGGHHHHHHHHGHGHHHGGGGGHFHHHHFHHHFFHHHHHFGCGGEHFHHFGGHFHGGGGGGHHFEEEAFEFFDFHGHHHHGGGGGGGHH0DGGGGCGHCC-FFFFFFFGGGGGGGGGGHHHHHGHHHHGHHGGHHGGHGGHHHGHHHHFHHGHHAFGGGHHHHHGHHHHFHFHHHHHECGGGHGHHHEFHFHGGGGGGGGFGFFGFFEFGEGHHHGHHGGDGGGHGFGGGGGGGGE@GCGGHHHGHHHHHGHHHHFHHGEGFFEGCE.ECCECEHCGGFFE/AABFFG0CFE0BFFF9CFGG.F/BBBFFGFGGGFFFFFFBFEDAEFFFFFBFFFFFFF0;FEBF: +@M01368:8:000000000-A3GHV:1:1112:10272:7828/2:GTATCCGA +GTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +BBCCBFFCCCCCGGGGGGGGGGGGGGHHHHHHGGGGGGHHFHGGGGGFGHGGGGGGHHHHHHHHHHFHHHHFHGFFHHGF?ECEFFFFFFHHHHHH?FHHHHHHHHHGFHHHHHHGGGFGHHHHFHHHHHHHHHHGGGFGFGCGGGGHHHHHHHHHHHGGFFHGHHHHHFFHFCGFHCCGHGHC +@M01368:8:000000000-A3GHV:1:1112:9832:16531/2:CTGTAATA +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBBFBBBBBFGGGGGGGGGGHFHHHHHHHHHHHHHHGHHHHGHFHHHGEEGGHHHGHHHHHHHHHHHHEHGHHGGGHGGHGHHHHHGHHHHGHHHHHHHHHHHHHHGHHHHHGEGCGHHHHHGHHHHHHHHHHHHHHGHFFGHGHHGGGDACDFFFFABFFFFFFFFFFD-BC?DA9.DFFBEA==B=?F.;ABBFBFEF-DAF/BFF9/FFFBB/9BFFFFFFF/BFBBFFFFFFF/9FEA?--B/;. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/2:CGCCTGTA +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATT ++ +BBBBAFFFFFFFGGGGGGGGGGFGHHHHHGHHHHHHHHHHHHCGHHHHHHHGHHHHHHDGHHGGAECHHGHHHHHHHGHHHGHGFHHHHGGHGGHHFHHHHHHFHHHHHHHHH2GHHHHGHGHHFHHGGFGGGHHGHHHHHFHHHHEFHHHHEFGFFHGEHCFGDFDFFFFFCFFFFFFFFFFFFFAFBFFDFFFFFFFFADCF?9?EFBFB9EF-A.;BFFFFFFFBFFFFFFFFFFFFBFFFFFFFFFF +@M01368:8:000000000-A3GHV:1:1113:13532:8618/2:GGAATCAA +GCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG ++ +CDDDBFFFFFFFGGGGGGGGGGHHHHHGGHHHGHHHGHHGGGGEHHGGHHHHHHHHHHHHHHGHHGHHHHHGGHHHHHFHHHHGCDCGHHHHHHHHEHHHGHGHHHGFHGGHGGHHHHHHHHFHHHFHHHGHHHHHHHHHFGGHHHHGGGEGAFHHGHHGGHHHHGHFBGFHGHGHGHGGHGGF@DAFEFBECAB=A.0BFFFEDF=A9.@D.-AAFFFA-:-..:.9/0:;0..-..0000: +@M01368:8:000000000-A3GHV:1:1113:21679:18011/2:GATCACAG +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGAC ++ +BCCCBFFFFFFFGGGGGGGGGGHHHHHFHHHGHHHGFGHGGHGGHHHHHHGHHHHHHHGGGGFHHHHHHEGHHHHHHHHFGGFCGEHFHFGEGHHHFGGGGGHHHGGGEHGGGGGHHHHHHGDCCCGHHHHDGGGGCD/FCC->DFFF. +@M01368:8:000000000-A3GHV:1:1113:5741:16959/2:TAGTAAGT +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +BBBBCFCCCCCFGGGGGGGGGGHHHHHHHGHHHHHHHHGHHHHGHDGHHHGGGGHHHHHHHHHHHHHHHGHHHHHGGGEGGHHHHFHHHHHHHHHHHHHHHHHHHHHHGHHGHHGGGGGHHHHHHHHHHHGHHHFHHHHHHGHGHGHGGGGCGGFGGFFFFFFFFFFFFFBFFFFFFFFFFFFFFAFFFFEAEFFFFFFFFFFF9BFFBFFFFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFADAB-/BF. +@M01368:8:000000000-A3GHV:1:1114:10130:11959/2:CGTTCCCC +ATCAGAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAA ++ +BCCDDFFFFFFFGGGGGGGGGGGHHHHHGGHHHGGGCGGHGHGGGGHHGGGGHHHHHHGGGEGGHHHFGGGGG?E1FE?/EEHHHHHGHHGHHHHGHFHGHGHHGDGGFG2FF2?GHHHHHGCCCFHGHGHHHHGHHFEHHFGHHGHH<1=DGHHHGH +@M01368:8:000000000-A3GHV:1:1114:14540:5315/2:CTTTAGTA +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCC ++ +CCCCCFFCCDCCGGGGGGGGGGHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHHGHHHHHHHGHHHHFHFHHHGGGGGHHHHHHHHHHHHHGHHHHHHHHGGGGGGHHHFHHHGHHHHHHHHHHHHHHHHHHGHGHHHGGGFGHHHHHHHHFHHHHHF?1FHHGHGHGHGHHGGFFFFDBFBE;BCC.:BFFFFFFFFFFFFFF;AFFFFF-=-.AEDEFFFFF..9A;9FFFF0FFFFE00FFF0:BA. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/2:TAAATAAG +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGTGG ++ +CCCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHDGHHHHFHHGHHGHHHHHGGGGEHHHHFHHFF5FHHFEGHHHGDHGGHGHGFGGGEHFGHHGGGGGHGHHHGHHFHHB3FGHHFGGGG?GFFHCCEBGFFECCDFEGFCFGCHHGFDDHHHGHHCFGGGGGFBFDGFG?-:..AFG.-C0C009;:00;00:9/:CEFFF?AE::9;9?0:FEF0;0..--./00::B/090000000;A.... +@M01368:8:000000000-A3GHV:1:1114:16639:15258/2:CCTAAATA +TTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCGCACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATG ++ +CDCCCFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHGHHHHHHGGGGGHGIHHHIH5DEGHHHF?FGHGGHGGHEGGHFHHGHGEHHGGGGGFFFGHFBG2GHEBGHHGHGGEG/GFGABEDFGHEED?GGHHFFGGGCFEGD/GFHFFGEFGCGG?CC??D-EF@EEEFGCDDBBFGGGEBBFFF09090A.BFGA.9CCA0;EBAB00BBFF.@-./;BB;BFFF0:00099AAFFF0 +@M01368:8:000000000-A3GHV:1:1114:2404:13066/2:TCCTACAA +ATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGC ++ +CCCCCFFFFFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_1.fq b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_1.fq new file mode 100644 index 000000000..d8a47fcee --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_1.fq @@ -0,0 +1,388 @@ +@M01368:8:000000000-A3GHV:1:1101:14518:9998/1:CATCACGA +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGAT ++ +AAAAAFFFFFFFGGGGGGGGGGHGGHHHHGHHHHHHHGCGHHHHHHHHHHHHHHHGGGGGHHHHHHHHHGHHGFHFE5BGEEHFGGGHHHHHHHHFBHHGGGGFHGHHFGHHHHGHHHHHHGEGGGGFHFHGEGHHGGCDGDGHGGGDGGHGGCGGGHGHHH/ACDG?.1FGCDCCGCA.CC@CDCHFHGFFGGGEBFGAB//CEFBFGG.:;D;;A0AFFFFFB..:@ABFF//;BFFFFFBF/9D:A// +@M01368:8:000000000-A3GHV:1:1101:18422:19051/1:CTACAAGC +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACG ++ +CCCCCFDDDDDFGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHFHHHHGGGGHHHHHHHHHGHHHHHHHHHHHHGGHGGHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHGCGGGHHHHHHHHHHHHHHHHHHHHHHGFDHGFHCFGGGGFGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF;FFFFFFFFFFFFFFFFFFFFFFFFFFFFEFBFFFFFFFFFF:FFF. +@M01368:8:000000000-A3GHV:1:1101:25545:21098/1:GCCCATAA +ATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATAAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGGCTTATTTAAGGGGAACGGGTGGGG ++ +33AA?DFD5BDFGGGFEBDGEGHEGHGEGHCEGGHHCHGHHFFHHGFGAGE53FF2FAFFGDE5FFFE5GFBFGAEE1GHHHGHHHEHE3FGHF@GEGEGGHHGG3FAGFFDE?EEE3GFEGFGFGGCG?GHHHFHGGGC@DHFFHD/AA@AAAAD2ADDFFGGGGGFGGHA?EAEFBEAGHFABFGG5FDF5DB1EEGAFDFB53FF5FH@G5FFEHGHEFHFFHBE333GF43GCGGGGE@0?BFGGB0B?FHGFDGGHHHBFFDEGGHGFFFDFE@<1>@FFFGHHHHFHEFGDABFFGG/@DCE;>=EF?AEFFFF;9;=DAFFFFBBFFFBFFF//;BFB.:FBFFBB/BFFFF/BFFE?EFAFEF9 +@M01368:8:000000000-A3GHV:1:1104:11928:24197/1:CCTCGCTC +ACGTAGGTGCGATAAATAATGGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATA ++ +CDDCCFCFFFBCGGGGGGGGGGHHHGHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHGGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHGHHHHGHHGHHHHGGHGEEGGGGFHHFHHHGHGEHHHHHHHHHHHHHHHHHGGGGGGFGGGGGGGGFFGGGFGFGAEFEFGFEAFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF@D9 +@M01368:8:000000000-A3GHV:1:1104:12288:20635/1:CCTACAAG +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGCCGCAGCATCTGTCTTTGATTCCTGCCT ++ +ABA?AFBAB2>AFGGGGFFGD5GGHGFFHGHEGGGGHHHHFFHH5FHGHHHFFHEFHHHHHHGGHHHHHGFHGGHGGGGFHGGGFBHHHFGEGHHHHGHGGGGECEHHFHHGHHFFHFGGGHHHEGHDGHHGHGHFHHHECGCBCHHGFHHFHD1GFHEFHEF?GDCFFEFE0A@;@>BD/9BFBBBBFDFFFF99D=?>DDBFF-AFFEBB9BBEFEFAFFF//-@---;;FBBFBFB///;99999BA9 +@M01368:8:000000000-A3GHV:1:1104:13832:4398/1:GACAGATA +CACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAG ++ +AAABABCAFFFFGGGGGGGGGGHFHHHHHHHHHGFFHHGGHGGGGGHHHHHHHHHHFHHHHGHHHHHGGHGHGGHGGGGGGGHGFFGGGGDGGHHHHGGGGFGGGGGCFGGEGCDGGGGGGGGGGGGEGF? +@M01368:8:000000000-A3GHV:1:1104:23670:4161/1:CGACATCT +ATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCC ++ +AAAABFFFFFFFGGGGGGGCGBBGGHHHHHHHHHGHHHHHHHHHHFGGHHHHHHGGFHHHHHHHGGGGGFHHHGHHHHHGHHHHGHHGGGHGGGGHHHHHGHHHHHHEGGGFHHHGFFDGEGHGHFHGHHGEGGGHHBGHGGHGHGGGGG/@FCDFDGFHGGGDFFHFGFFGGGGGHHHHGGGGGGGEGCDG?GGBFFFEE00BFFGABBBAFGGGEGEA.9FFF/./;BFBF./AAF/BFFBBF/F/BFB +@M01368:8:000000000-A3GHV:1:1104:24927:22253/1:GTAATATT +AGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTAT ++ +AAA?AFFF3DFFFGGBGFF3EAEEEHFHHFHHHGHHHHDGHHGAEFGHHHGFCHHGHHHBGHHHAEGGHGGFHFBFHHHHHHHHHHFHH1EEHEEHH1FFDEEFCGHBGHHFHEHHHHHH1FCGHHHHEEFGEEGFFCHHH11>GHHF/FG2DGGCGAGGHGGGG@@@BEFFF?@@@FFEFFFFFF?@@FB@BB@FFFE=;==---A9EFBBB/;E;A9B/B/FFFEF/B///;/;9/A/;/9BFFFBFBB +@M01368:8:000000000-A3GHV:1:1104:4705:7727/1:TCCTACTT +CTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +BBBBBFFBFFFFGGGGGGGGGGHHHGHHHGHHHHH6GHHHHFFGGGHHHHHHHHHHHHHHHGGFGGGEGGGHHHHHHHHHHGHE3FGGGGHHHHHFHHHHHHHHHHHHGGGGGHHFHFCGFHHGGGGGGGHHGGGGHHGGGGGGHHHHGGGADCHHHHGDGGGGGGGGC@DGFHEHHHHHHGHHHHGFGDEGFGFFGGGGCFGBEGFGGGFG;C.BFFFFFFFBFBFFFF/F?.AFFF/BFFEFFFFFEFF +@M01368:8:000000000-A3GHV:1:1104:7756:4776/1:CTACAAGC +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +CCCCCCFFFFFFGGGGGGGEEFHHHHGHGHHHHHHGGHHHGGGGGGHHGHHHHHGHHGHHHGGFHHHHHHHHGHHHFHHGHHGFGGGGHHHHHHHHGHGHFFHFHHHHHHGGHGFGFHHHGHG?FGHHHHHHHHHHHHHHGHGHHGHGGCDGFFHHHHGHHHHHGHHHGFHGHFHGHGHGH/@CABFFFFFFFACAFF?BBFFBFD-@-.D>FFAF.F.:9---;AADFFFFFBEFFF:9FFFFBBFFFF/ +@M01368:8:000000000-A3GHV:1:1105:11310:21761/1:ACTTGGGG +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTCGGATACAGTTCACTTT ++ +CCCCBFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHGHHHHHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHGHHHGHHHGHGHHGHHHHGGHGGG=FFGEHHHHHGHFGGHHGHHHHHFHHHHHHHGGHHHHHHHGHEHHGHHHHHGGGGF9AGE?DEGFFGGGGGGGGGGGGGGFFFF/9FFBFFFFFFFEFFFBFFFFFFFFFFFFEFFF0 +@M01368:8:000000000-A3GHV:1:1105:11578:14676/1:GCTCCGGG +ATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATGTC ++ +CDDDDFFFBFFCGGGGGGGGGGHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHFGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHHHHHHHHHHHHHGHHHHGGGGGGHGGHGHHHHHHH;CHHHHHHHHHHHHHHHGHGGGGFGGGFGGGGGGGGGGGGFGGGEGGFFFFFFFFFFFFFFFFFFFFFFFFF/FFFFFFFFFFFFFFFF0 +@M01368:8:000000000-A3GHV:1:1105:13575:19255/1:GGTTCCTA +TTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGTTCCCGTGAGTGGTTAATAGGGTGATAGGCCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATG ++ +AA1A1DFFFFFBGG3A111FFAEGDDBGFDHF00F01BBA00BFGEHFBFFA1FABB0FAE?CFHF1BGFHFB0011F121E//>>1F10>B?EFHGCC/?/BFG/EEGFFEE//BCFDE0?E@@B/?11AAFFFFFEAGGGFGGAA6FHDGGCGFHFFHFHFHHHHHGDDDFFFHGFFHGBEGEGHHHFFFHGEEAEGHHHHHFHHHFHGHFEDGGEGBEAGEFHHFFHHHHHHGGHHHGHHGBGHHFHHFGHHHHG?CG?AFHH1FHHHGHFHHHF?DGHFFHCGAGEFHGCBBBB?BFFF?B-B.9/BFFFFFB=-AD?..@FFFF@@-@@?AFD.FFFBBEEBD9/:FFFFFBB/:FF9BF/BF.BBFF/: +@M01368:8:000000000-A3GHV:1:1105:21099:2895/1:TTATTATT +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTT ++ +CBCBBFFFFFFFGGGGGGGGGGGGGFHHHHFHGHHHHHHFHHHHFGFHHHHHHGHHHHHHGHHEHGGGGHHHHHHHHHHHHHHHHHHHHHHGGHGGHHHHHHHHFHHHHGHGHHHGGHHHHHGGHFFGHGCGGGHGHHGHHHFGHHFHH/FGGGHFGFEGGCFCCD;B@DFFFFFFFFFFFFFFFFFFFFFFFFF;F.BEFADFFFF.AEFFFFFFE;D.;:B00099:09BFBFFBFF.0:000BFFBF0 +@M01368:8:000000000-A3GHV:1:1105:26469:19245/1:GGGGTAGC +TTATGATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCAAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATG ++ +BAAAAFFFBFFFGGGGGGFFGGHHHHHHHHHHHHGGHHGHHHGGHHHHHHHHHHHDEGGHGHHHHHGEDHFHGFHGGHHGGHGGEHHHGHHGHHGHHHGGEGGGHGHGHHHHHHGHHHHGHGGGGGHFHGGGGHHGGGGCDGHHHGD>A@FFFFFFFGGGFEECFGGFFB5GBHH5DFH5GBEEAEFHFHHF3F3GHFHHHEF3GAEHBGFHFFEFFHHHHFFB31FGGEGFHGEHHHHHHHHHHHHHHHHHEEEEGHHHFFF3GF3FGF44BBGEHHHHGG2B/BGGHE;B=.9.;.BBFFF..;A;/B/;B//;;//BBF/ +@M01368:8:000000000-A3GHV:1:1106:22927:3863/1:AAGACAGA +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTA ++ +A>ABAFA?D@AFGGGGFGGGFGFHHHFFH4BCBGHHHHGFFF3G5BF3322EEAFHHHHHHAB5GHFHEHFHHH3BEEHFGF5@13FDF3GDGFHHFGHHHGHHHGFGGHHFCG//?/EGHHHG3F4BFFGHHHEDGFHHB/B/?FBF<@-9?BDEFFF?B--?DFFFB9FA>B;A.BFDB?AB.--@;-.FFAEFFFF9AE;DDF +@M01368:8:000000000-A3GHV:1:1106:23625:4236/1:CACTTTAG +TAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTA ++ +@?AAAFFBFBFFFGGFGFGGGEFCGGHHHHFGHGHFHGHHHHGGFGGFGHHGHGHHHHGHGFFHHGGGGGHHHHHHHHHBFHHEFHHHHHHGF?FAGHGFHHHGDGFHHGGGHGHFHHHGHHHGHHFHHGFFGFHHHGHHHHFFHHHHH/FGHHHHGHGHGBFFF9 +@M01368:8:000000000-A3GHV:1:1107:14451:26748/1:AGCTAAAG +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BABBBFFDABBBGGGGGGGGGGHGHHHHGAGHGGGGGHHHHHHHHGHHHHHGGGGGGFFHHHHHHHHHFHHHHHGGGGCHFHH3FEHHGCGGGDGHHHGFGGHHGGGGHHHHHHG/DGGGHHHHGGGGGCCHGG?CGG1GHHGHHHHBGHHHFHHGHHHHGGADAD00ECEGHEFHHFFAEFFFFFGGFBFBFFFGFFG.;B/99;BCFGGGGEFFFFFFEDA./:ADEB?FBFFFF;FFEBFBFFB./9. +@M01368:8:000000000-A3GHV:1:1107:18714:24788/1:GGCCCATA +GTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGA ++ +BBBCCFFFDEDEGGGGGGGGGGHHHHHHGGHHGGHGGHHHHHHHHHHHHHHGGGGGHHHHHHHHHHHHHHHHHHGGGGGHHHHCFGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHHHHHGHHHHHHHHHHHGHHHHGGEGEGCCEGGHHHHHHG:CAFFGGGGGGBFEFGGGGHGAFFGGFGGGGGGGEFFFFFFFFFEF/EDDFFFFFFFFFBFFFFFBBFFBBF/ +@M01368:8:000000000-A3GHV:1:1107:21355:8333/1:GTATCCGA +ATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +ABCBBFFFFFAFGGGGGGGGGGHHHHHHHHFHHHHHGGGGGHHHHHHFHHHGHHHHHHHGGGGGHHHHFFGHGHGGGGGGGHGGEGGGHGGGGHHHHHHGGGGGGHHHHGGGGGGGHGGGGGGHGHHHFHHHHHHHHGHFFHHHHGGHGEGHHGHGFHHFHGHCEFHEGHGHHHGHHHGGGGGGCFFFFBFGGFGGGGFBG?FDGGGEGFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFBFF.AA/9 +@M01368:8:000000000-A3GHV:1:1107:22864:15712/1:GTAATATT +AATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTC ++ +BBBBBFBBFFFFGGGGCEGGGGHGHHDGFHHHHHHHHHHHHHCHHGHFGBGDFGE?GHHGHFBHHFHHHHHHHHHGHFGFGHGHHGGC@DCFGHHGGGGGGGHHHHHHGGGGGFGGGGFFGGGGFADGFEFFFFFFFFFFF9;FFFF/BFFFFFFFFFFFFFFFFFFFFFFFEFFFFFFEAECDFFFFFFF +@M01368:8:000000000-A3GHV:1:1107:24817:14233/1:CTTTAGTA +CTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACAT ++ +3AABABFFBFFFGCFGGGGGGGHHHFGCFGGGFFGHHCGHHHGHGHGHBFFHHHEDGGFGFGHHFFFHGGEGHFHHGHFHGFFHHHFGHHHFHACECEHHHBGFHGFHHHFHHF4GFHFHFHEHGGE/EG:A-CFGGFGADGGGGFGGGGDAAAADFA.-AFFECFDAAFFFFEFFFFBFF;D;BFFFB/;BFFFFFFFFFFFFFFBFFBF/;//;BFFFF?FFFFFFEDAFFFFFBF//:BFBACF--9/ +@M01368:8:000000000-A3GHV:1:1107:24830:14440/1:CTTTAGTA +AACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACC ++ +ABBBA@FFFFBBGGGGGGGGGGHGHHGHHGHHHGGHHHHHGHGHHGDHHHHHHAGGGGFHHGHHHHHHGHHHHHHHHHHHEGAFGFHFHHHHGEGHHHHHHHHHHHHHHHHHGGHHHGEFEGGHHGHHHHHGGHGFHH/?GHHHHGFGHGFHCGGBBDAFFFEFFFFFFFFFFFFFF=CDDADDFFFFEF=BFFFEFFFBFFFFEEBF./:FFFFFFFFFFFFFFFFFFFEFFFFFFFFFFF/BFBEFFC- +@M01368:8:000000000-A3GHV:1:1107:26478:23602/1:ATCAAAGA +GCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTG ++ +1AAAAF1B13BBBEGGGFGGGGGGHHDB1BGFHHHFGFGGG0F00BGBGFGGF1GBGB1BGCGAEE/FGFHGHFHHHHHBFF1B0FGGF//F//FGFGFFF/1@B1DFHHHGGEFEDHFDFAFF0B//1FDD1GFFHHDF?1BD>GF/GCAC0C@?@-;99BBB->@--;-B//99B--9-BF=A--A-:A----9AA9AFBFBBB?E@BBFFFFF +@M01368:8:000000000-A3GHV:1:1108:11059:23181/1:AACTGTAT +GTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGAT ++ +CCCCCFFFFFFFGGGGGGGGGGGHHHHHHHHHHHHHHHHGHHHHHHHHHHHHHGHHGGGGHIIIHHHHHHHGHHHHGHHHGGHGGHHHHHHHHHHHHHHGGGGGHHGHHHHHHHHHHHHHHHGGGGGHHHHHFGHHHGGGGGGHHHGGGGGHGGGGHHHHHHGGGGGGHGGHEFGGGGGHGGG-ECHHHGGGGGGGGGFGFFGGGGFGGGCF?EFGG0;BFFFFB?9AAFFFFFFBF;BBFFBFFFFE?F/ +@M01368:8:000000000-A3GHV:1:1108:12233:13498/1:GGTTCCTA +TAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAG ++ +BCCBAFFBCCCCGGGGGGGGGGHHHHGGGGGHHHHHHGHGHBGFHHHHHGGGGGHHGGBFGHHGGGGGGGHHHGGGGHHGGGFHHHHHHGGGGGGHGHHGGGGGGGGGGGGGGHHHHFHHHGHGHHHHHHGHGHHGGFGGGDFFGGHHHGHGH/FHHHFHGHGHHGHHHGHHBAAAA3BDFFFFDGBFFEEGGGGHHGHFHHCFHGHGHHHGF3BFGFHGFEFHFHGH3EGFC1EEGBFGBHFGGFFHHHGHFHGHHGHGGHCEHEBCFF3ED3@GH4FDEG12FFHFFHG/G3FGA/@EFEFCG33FFGBBGHFHH/?BFBGFGFAGC2C/@-;@-;BFFEFADF?DFFFFFF?;AFFA;AD;..FEFFA--;9;D.9BFFBE?;.;///://///99//BB/9;F./B/ +@M01368:8:000000000-A3GHV:1:1109:25237:11722/1:CATCACGA +CCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCA ++ +AABBBFFFFFBBF5BGGFGABGHGGAEFGFHHHHFHCHFHHBFGGGEHBGGHFFFFGFAEF5FHH?EGGF5AEG3?EBFHD?C/EFHFFEGEE?CFGGGHHFHB3EEFG?EEGHCFGGGGGGGECCFHHGDFGGGGGEFGC?EGHHHB0CGHHGCGHHHHBEHGHH.::ACA;FECFGGGGGFFFEFGGGGGGGFFBBBFGBFFFEFFFFBFFFFFFBBFBFFB9.. +@M01368:8:000000000-A3GHV:1:1110:14751:26540/1:ATGTTCGC +TAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACTGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGTTGTGCACGCGATAGCATTGCGCGACGCTGGCGCCGGCGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTG ++ +AAA?1CFFFFADGEEGFGB1112DGDGHGFGHHCG/ECEBGGHDFGHHFHGHEB1BCGFFE2EGHHGHFFFHHBFFHEFCGGHHFHHHHH111BFFHGHEHBEHGGECEFHGFHFGGDBBGHHBHHHH0GH22FGHGFFFH1BFCG0F@FGG11@GDHFG1D/1FGFHH/FCG.>0><-<@CCFFG.CC-@C?C9FFF0C---;------;9----9-9@-AAFF9B9---9-/;B9BF/9BB//B/;/// +@M01368:8:000000000-A3GHV:1:1110:15519:10008/1:GGTTCCTA +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACC ++ +BBBBBFFFFFFFGGGGGGCBGGE?GGGHHHHHGHHBEGGHHGGGGGHHHHHHHHHHHGGHHHHGFGGGGHGHGCFGHHHGGGCGGHGHGGGGGHFGGGHHHHHHGCEFGGHHHHGGGGGGGHGG/CEGHHHHGFHHHGFHHGFFHGHGHFGGEGFDDGGBCGHHGFHH/CHHHHGHGHF0CFGGGGGGGFFFFFBFFFFFFGFFGGF?DGEDEEFEFFFF?FFFFFFFFFFFFFFFBFFF.BFFFBFBBA; +@M01368:8:000000000-A3GHV:1:1110:16559:7507/1:GCCCACAC +CATTCAATTGTTATTATTATGTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAACTGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATC ++ +ABBBAFFFFFFFFGGGGGGGFGGGGAGHHGCHHGHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHFGGGHHHHHHHHBDHHHHHGGHFEEGHGGHHHHHHHGHHHEHFGGGGGGHHHF33FGHHG3GDDGH//EEGHHFFBF?GHHFCC@DGFCGGB?DGHAFGGHHGFH0E??<@DGHGGCFGGF?DGGGFFGGGGGGGG.C/0BBF?FBBEGG0FFF.AA9;B9/E////99;;:.//:FFFFBBF//9 +@M01368:8:000000000-A3GHV:1:1110:16700:6843/1:GTTCCTAC +AAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAA ++ +BBBBBFFFFFFFGGGGGGGGGGHHHHGHHHHHHHHHHHHGGGGGHHHHHGGHGHGGGGGGHHHGFFGHHGGGGHHHHHHCGG@FGHFHFEGGGGGGHGGGGDGHHHHHHHHHHHHHHGHHGHGHHGGGGGCGHEHGHHHFHHHFF.DGHHHHHHGHHHHHHGFGHGCGHGHHHHHHHHGHHHCD?:A::FCDGEGFGFFBFGBFGGGF00CBFFFF/ +@M01368:8:000000000-A3GHV:1:1110:18014:7856/1:CATCACGA +ATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCA ++ +AABBBFFFFFFFCGGGCGGGGGGHHHHHGFHHHHHHGHHHGGGGGFHHGHFGGHHHGGFGGGHHGGGGGHHGGGGHGGHHHGGGGGGHHGHGDGGGGGGGGB/ACC=@--AFBFFB?=BFDFFF//FDB;-9A-AD-.A.A=?-9-:B/AEB/BFF.A;DDFFFBBFFFF/BBFFFFBFF9B; +@M01368:8:000000000-A3GHV:1:1111:13195:14562/1:GTATCCGA +ATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACCAGATG ++ +ABAAAFFFFFFFGGGGGGGGGGGHHGG4FDFGFGGCGGGHGHG?EGHEGFFDHFHHHHGGFE@EHHGEEEGFCCEFFGFG/EHHHHHBFBGGHFHFHEHGHEFGGGED/EFDEFFEHHBGHHCFFFDFGGHHGFFFHHHHGFG>0<0DGGFHBGHFBDFGHGFFGGAGHHGCGBHFFHHHFFFBFGGGGF/:FFFCB9F9FF0FEFE?FF +@M01368:8:000000000-A3GHV:1:1111:14287:20817/1:ATTCAATT +GCCAACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTCATCGCACCTACGTTCACTATTACAGGCGAACATACTTATTAAAGTGTGTTAATTAAT ++ +>>A3>AAAACFFFGFGFGGGGGHGHHHHHHHGGGGGHGHFFCGHHGBGHFHHHHAGHHHHEHHAGFFEHEAE?GHHHHEGFFFDGHGHBFFHFHHHGHGHGHBECG@@@EHGGEGCGGGGFFGGGG?BGGGGGG.-C.FEDCFFFEFFFAF/99BEFA.:9BFB/9FFFEFFFFFFEFFF/FBBFFFFFFFFFFFB//;.@@//;DFFFF//BBFFFBF;A;DF=>B//;9B//B/;/;9//9//;B/:B9 +@M01368:8:000000000-A3GHV:1:1111:23624:14516/1:CGACATCT +GTCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGGGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAG ++ +3>3AAFFFFFAFGGGGGGGGBGHHHHHHGGHGGHEHGHADFHHHHEGGGHBGHFFHHEHHGHFHGG5FBEEGEGHHHGHHHEFDGHHFFGFGGHHGHHHGHBHGHFHFHHGGGGFCFBGFGE?GFBECEGDGHEHGDGCGHGC/DF@GHGFFCGGGGFFFFDD?@C@GFEC?-ADHFFHBGHFBHFG0CC//.;B0/CA.;AA.;@.AB/9BB/A/.AFFFE/BFFF///9B/FBDE9/;99/B/BFFEF/ +@M01368:8:000000000-A3GHV:1:1111:7437:24508/1:ACATCACG +ACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCAT ++ +CBCCDCFFFFFFGGGGGGGGGGGGGGHHHHHHHHHHHHHHHHGGGFFEHGGHHHHHHHHHHHGHHGGGGGHHHHHHFHHHHGHHHHGHGGGGGHHHHHGGHHHGGGGGGHHHGGGGHHGGGGHHHHHHGGGGGGHGHHGGGGGGGHGGGGGCGHHHHGHHGHHHHHHHEDHHGHGGGGGD;BEGGGFFGGGGC:CFGGGGGGGGGFGGGFF +@M01368:8:000000000-A3GHV:1:1111:8665:25542/1:CTTTAGTA +TCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTGTCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +AA3AAFFFFFFFGGGFGFFGGGGHGH4AGGGFHHCGEE2FGHHHHHHHHHHGFHGF53FHEGGFAF5CFHHGGFGHFHHGGHHHCHHHHHHHFHHGH?EEEG1FFFEHHFHFGGHHGG?F4FBGHGHCHEF0//-9--;0CFGG?@BGDGFFFFEFBBBDA?FFBFFFF=B;-9.AA9EFFFF/;9BD.//;9/9/B:/:BFBFFBFFF/B:BFF//;/B/FFFBFF.A-BFFFBA/F//BFFFBF/;/A- +@M01368:8:000000000-A3GHV:1:1111:9655:13916/1:TTAGTAAG +GGCCCATAACACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGCGGTGTCCACGCAATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGA ++ +1>>1AAFFFFFBGGFE1EEEEGGHGHHH2FGHHHFGFGHGCFGGGEFHGGEGGHHHHGHEFBFEGHHHGHHBEHHHHGHGFHHHGGGGHHEGGGGHHHGFHGHHHH1FHHG?G/AGF1GBFGEFFHF2FDD0FG--99@=---AAABA-BF/B?A@F-9BBFF//BB/9/ +@M01368:8:000000000-A3GHV:1:1112:10272:7828/1:GTGCTCCG +GTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGC ++ +AAABABBBBBBFGGGGGGGGGGHGHHGHGHHHHHHHHHGHHHGGHDGHHHGGGGHHHHHHHHHHHHHHHFHGHHHHGGHGGHHHFHHHHHCGHFFHHHHHHHHHHHHHGHGEFGAEEEEHHGHHGHGHHHHHHHGHHHHHHGHGHFFBC/BA?BGGGFFFFFFFFFFFFFFFC-@DDFFFFFFF +@M01368:8:000000000-A3GHV:1:1112:9832:16531/1:GTATCCGA +CTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGCTGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCTTGAAGTAGGAACC ++ +AABABFFFFFFFF4GGGGEBGEFGHGGHGHGHHHGGHFBGFGGGGGHHEFHGEHFHFHEHHHHHGCGGGHFHHCFGHE@1EEEFFGB?EEEEHBGGGCHHGHHBEE@>EAHHFAEBDGGGCEFF?CEGFFHHHHHFHHHFHGHCGCAHHF<..C.D=0CD.GFHHHG.CAGHC:CHB0GGGFFB0:CFA.A-;9.;000CBBFFBFGA.9AA;A;EDDE.ABBFFFF9;BEFFF/BF//9/B//9:B//.. +@M01368:8:000000000-A3GHV:1:1112:9832:6701/1:GCTAAAGT +CGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGACCCTGAAGTAGGA ++ +AABBBBFFFFFFGGGFGGGGGGHHHGGHGGHHHHHHHHHHHGHHGGGGGHHHHHHHHHHHHHHHHHHGGCGDHHHHFGGHHHGGGGGFGGHGGGGHHGGGGHHHHHHGGGGGGHHGGGGDGGFGHGGFCDCHHHHGHHHHGHHFAGFGGEHFGEG.C1>11F1D1DDFFFFGGG1FH3GHGHGHGHFHEC?EC0B1FBGFB1GHHH21AF2HH2FEGEHAE10AAE/>/FFHE?/E/?E1@EFFH?E@/EGGG//B11B//<@@C0F/<0AAAAFFFBFFFGGGGGGGGGGHHFHGHHHHGHHHHHHHHHHHGGGGHHHHFHHHHFHGHHHHGAFFEFHEGHHHHHHHHGHEHHGGFGGGHHHHHHFHHHHHGGHHHHGGGGGHFHHFF?HHGGFECEFFGHFFGFHGECDGHGBGFHGDF@@?CGFHCEGGGFD.CCC?EGHBHHHFHHFBCFFGEB/CEGGGGDAA.90C9CEBFGGBBF/9.9FBFFFBBFF//99FFFFEABF//99FFEFFFBFF +@M01368:8:000000000-A3GHV:1:1113:5741:16959/1:GTATCCGA +TAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGTGGGCTATTTAGGTTTTATGA ++ +ABBBBFFFFFFFGGGFGGGGGGHHHGHHGGHBGHGAGFFCAFGHGFFGHHGFHHHHHGGGGGHGHHHHHHHHE3BFFHHHGG0EDF@GHFFGGGHGGGGGGGGGGGGGHHGGEEFHGFHHDDG@DGGGHHGDGGGGGHGG?CF?HHGHHHGHGHHHFFHGGGHHHHGGCD.;0A33>FFFFFF@FFFGGGGFGGD4EGGGGGHHGFFGHFGGHHHFEFHECFHHHEHGAGBCCGCCEGGHGHEGFBFHFHHHHGGGHFHGHEGGGFEGEGG??@DBGHGGC-@FFGHFHFHB-??DA-DD@9:BEBG@B?E?A.ABBFBFA??F.FF/BF +@M01368:8:000000000-A3GHV:1:1114:14540:5315/1:CACTTGGG +CTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTT ++ +AABCCFFFFFFFGGGGGGGGGGHHHHHHHFHHHHGHHGHHGGGHGGHHHHHHHGHHHHHHGGGGGHHFHHHFGHHGGFHHHHHGGGGGHHHGHGGHHHGGGGGGHGHGGGGHHGGGGHHHHHEGDDFGFFFHHGGGGGCDAFCFGFDHHHHGGHGHHHHHHBCGEHHHHGGHG.ACGEHGG0CBFFF:A;BB0;09CGF00CFFFE0AA?//CFFFFFFFFFFFFFFFBEF;A.-=A--:BBFB90;;FE. +@M01368:8:000000000-A3GHV:1:1114:15066:16302/1:TTATTATT +TAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAACGGTTGTTAATTAATTATTGCTTGTAGGACA ++ +BBBBAFFBDFBFBGGGGGFGGGBGFFFHGFHHGFFFHGHHHGHHHHFFHHHGHGC?AEFFHEFBFFFGHHHHH1FDGFFHGHGHFEGCGC-<>ABFFFFFFGGCGC1BBF1GHHHBHHHHGFHGH1A100AA/GGEHGFBAA1FFD2FHHHHECG2F1BB/E0FC/A>EE/FGGFGEF1EGBBEHHCGGGHBGEHFHE0B?E--;C?CCGGG@A@GBFBBBB09?@??A-AB--ABE@=-=-9AE9A;FFFFFE=9-//;//;9FF/////;;///9B///;/B////9FFBB;--A@-;/9;9-:-/;;FFFE9BF?@;-9-99/B9F/://///99/; +@M01368:8:000000000-A3GHV:1:1114:2404:13066/1:ATGGATCA +TCCTACAAGCATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTG ++ +CCCCCFFFFCFFGGGGGGGGGGHHHHHGHHHHHHHHHFFHHHHHGGGGHHHHHHHHFHHHHHHFGGHHGGHGGHHHHHHGHHFHHHHGGGGGGHHHHHHGHHHHHHHHHHGGGGGGGHH?FGHHHGGGGGGHHGGFGGHHGGGGHHHHHFGGGGFGHGHHGGGGGGGHGGGEGGHHGHHHHHHHHHGFBFFDA0FGGGFFGG0:EFGGGGGGGG;AEBF0B0BFF diff --git a/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_2.fq b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_2.fq new file mode 100644 index 000000000..51b6608f0 --- /dev/null +++ b/sources/bin/tests/test-data/fastp_test/test-data/out_bwa_umi_read2_2.fq @@ -0,0 +1,388 @@ +@M01368:8:000000000-A3GHV:1:1101:14518:9998/2:CATCACGA +TGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGAACATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGACATAATAATAA ++ +CCCFGGGGGGGGGGHHHHHHHHHHHHHHHHGFHHHHGGGGGHGFHHHHHHHHHHHHHHHHHHHGHGGEHGGGGCGGGHHGGCGGGGGHHGHHHGGGGGGGG.BFFFGAGADFGAFDGFGGCFFF;DDFFFFFFFFFFFFFFFFFFEFFFFFFFFFFFBFFFFFFFFFFFFFFFFFFF09FFFE00;BE@;DABBFFFFFBBFB00;F:9;FFBFFF9BFFFFFFFFFFFFF90/::BFFFBF0 +@M01368:8:000000000-A3GHV:1:1101:18422:19051/2:CTACAAGC +ATTAATTAATTAACACACTTTAGTAAGTATGTTCGCCTGTAATATTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGGGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGG ++ +FFFFGGGGGGGGGGHHHGHHHHHHHHHHHHHHHHGGGGHHHHHHHHEHHHHHHHGGHHGGHGGHHHHHHHGHGGHHHGGGGGHGHHHHGGGHFHFHHHHHGGGGGHBFFCGDHHHGGGGGGHGGGGGGHHGCGGGFGHHBGGGGGFFFHEGGGGGCDCCE@EFGHHHHFHEGHGFFHHGB;ECBFGGGEFEFFGF0AFGFGFFG.;;DFFFFFFFFFF090BFFFE?FEFBBFBFFFB990BF +@M01368:8:000000000-A3GHV:1:1101:25545:21098/2:GCCCATAA +CACTTGGGGGTAGCTAAAGTGAACTGTATCCGACATCTGGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTTCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCAACCTATGTCGCAGTATCTGTCTTTGAT ++ +FFFFGCGGCGGGCGHHHGHHHHCGHFGHFHGFGGCDGGBD5FGFFFHFHGGGHAEBFGHHHEHGGFHBGGFHHHGGGEEFHHHFHFFHDHGHGHHHHFFHHGGFAEGFFFFFBGHHHFFHHHHHHHFHFHHFHGFHGHGA/<@EFHEHH1GGHFFFHG1>=FGHFHGF.GE//-AADEBGGGGFFCGGHHA5DFGAE?AAEDFHG2AEE1FBE00A1BGE0?E1FFGEEEGB4F43?EE/>///F??//@BCBAC<<.<<///FDFACF?FHFGC//??1B0<FF>DFCFDFFFFFFFFF-BBAFFFFFFFFE@D9B;FBFFFFF +@M01368:8:000000000-A3GHV:1:1103:25465:20010/2:AACCTAAA +TAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGTGCACCCTATGTC ++ +FFDFGGGGGGGGGGHHHHHHGHHHGFHHHHHHHGGGGGHHHHHGHHHHHHHHEHHHHHGHGGHHGGGHHHHGGGGGHHHHHEHFGEHHHEE14BGHHHGHGHFCE/EFGGGGGGHGGGGGG?FFGGGG.ADGGGFFDA.FFEC--;9BBBD?FFFFF +@M01368:8:000000000-A3GHV:1:1103:25519:6301/2:CTGTAATA +TTGAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATGCTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGGGATGTCTTATTT ++ +FFFFFFFGGGCAFGCGHGGGHGGGHHFHHHFHHGGGGGFFFHHHBHHHHG5BG5GFEEEE1FGFFGF1EGHGGG/BFHEF@EA1BE1@EED3?4DHGGGGEGHFFFDDG?DCDEG@<?@DGCAGC-;@DGFFHGCHEEFGGFGFB/;..BBB.CCE?A0FE0EBFF0FEF.;=DFFB//BFBF//;/:9BA.9FB9//;9//;9F;FF +@M01368:8:000000000-A3GHV:1:1104:13832:4398/2:GACAGATA +CTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGTGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTG ++ +FFFFGGGGGGGGGGGGGHGGGGGGGHHHGFGGHHFGGGHGHHGHGFGECGHHHHGGGGGGGHEGFGGGHHGHFHHHHFGHFHHHHGHHHHFGGFGG3FFGGHHHHHHH2?FFGHFHHHHHHHHHBGHDGC0 +@M01368:8:000000000-A3GHV:1:1104:23670:4161/2:CGACATCT +GGTTCCTACTTCAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAA ++ +FFFFGGGGGGGGGGHHFHHHHHHGHGHHHHHGCHHHHGGGGHHHHHHHHHHHHHHHGHHGHGHGGHGGHGHGGHHGFGHHGHHHEHHGHHHHHGHEHEHHHGGFGGHHHFHHHGHHHHHHHGHHHHG4EGGGFCBBCA?DGGGGGGCCAFFFFFFFFFFFFFFFFFDFFF.9@--=AFFFF;FBFFBEFFF9FBFFB9/FFFFFFB/FFFFFFFBFFFF/BBFBB/FFFE?.;@FFB?FBB// +@M01368:8:000000000-A3GHV:1:1104:24927:22253/2:GTAATATT +GAACGTAGGTGCGATAAATAATAGGATGAGGCAGGAATCAAAGACAGATACTGCGACATAGGGTGCTCCGGCTCCAGCGTCTCGCAATGCTATCGCGTGCACACCCCCCAGACGAAAATACCAAATGCATGGAGAGCTCCCGGGAGTGGTTAATAGGGTGATAGACCTGTGATCCATCGTGATGTCTTATTTAAGGGGAACGTGGGGGCTATTTAGGTTTTATGACCCTGAAGTAGGAACGAG ++ +FFFFGAFGG5GGGGHDGHHHHHHHHHHHHFHCFGC2F3BFGFGHBGHHFHEDHFGGGGGHHHG3F?GHHGGC/EFEHFGAEFFHGGAEHGGGG3EEGEEDHFHAAD@DGGGHG/AC1>GED-<<-.;C0:0C:C;GH:::::0B90;FFGEGFBFF0C.;9F0;0090;900;00FA9D.A...-9=BBFFFE/FE9;9E//BBBB.BBB///B/9/B..;. +@M01368:8:000000000-A3GHV:1:1104:4705:7727/2:TCCTACTT +CAGGGTCATAAAACCTAAATAGCCCACACGTTCCCCTTAAATAAGACATCACGATGGATCACAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCG ++ +FFFFGGFGGFGGGGGHHHHFHHHHHHGGGGHHHHHHHHHHHHHHHHHHHHHHEDEFGHFHHHHGHGHHHHHHHGHHHHHHHHFHGHHHHHGGGGGHHHGHHHHHHHHHHHGHHHHFHGHGHGGHGGGDCD.;FFGGGGGGGGFFFFFFFFFFFFF.>FFFFFF-BBEFFFFFBFFFFF-DDFFFFFFEFFFFFFFFFFFF?F///9FFFFF/;FFFFF?AADCFFEFAFFEFFFFFB/;B/A9 +@M01368:8:000000000-A3GHV:1:1104:7756:4776/2:CTACAAGC 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+CAGGTCTATCACCCTATTAACCACTCACGGGAGCTCTCCATGCATTTGGTATTTTCGTCTGGGGGGTGTGCACGCGATAGCATTGCGAGACGCTGGAGCCGGAGCACCCTATGTCGCAGTATCTGTCTTTGATTCCTGCCTCATCCTATTATTTATCGCACCTACGTTCAATATTACAGGCGACCATACTTACTAAAGTGTGTTAATTAATTAATGCTTGTAGGA ++ +FFFCGGGGGGGGGGHHHHHHHHHFFHHHHGGGGGHFFFHHFHHHHHHHHHHHHHHHGFEGGGHGEDFCDFHGHFG@@DGGHHHHHHGGGGCGGGGGEHGGCGBB?CF99EGFGGFGG?D9CFFFF/BBFFFFFEF9BFFAFFFFEFFFFFFFFFFFFFFFFFFFFF.FFBBFFFFFFFFFFFF-9;;;BFFFFFB9BFBFBFABFFEFFFFFFFFFF::BFFBFF diff --git a/sources/bin/tests/test_extract_galaxy_tools.py b/sources/bin/tests/test_extract_galaxy_tools.py index bb479f2dd..41db5677e 100644 --- a/sources/bin/tests/test_extract_galaxy_tools.py +++ b/sources/bin/tests/test_extract_galaxy_tools.py @@ -1,8 +1,10 @@ import json import os +import shutil import tempfile import unittest import xml.etree.ElementTree as et +from pathlib import Path from typing import ( Any, Dict, @@ -11,26 +13,45 @@ ) from unittest.mock import ( MagicMock, - Mock, patch, ) import pandas as pd import shared +import yaml from extract_galaxy_tools import ( + _load_tool_xml_fallback, + _normalize_repo_url, + _repo_name_from_url, + add_status, add_tutorial_ids_to_tools, add_workflow_ids_to_tools, aggregate_tool_stats, + check_categories, + check_tools_on_servers, + clone_repositories, + curate_tools, + export_missing_tools, + export_missing_tools_to_yaml, + export_tools_to_json, + export_tools_to_tsv, + export_tools_to_yml, + extract_missing_tools_per_servers, + extract_top_tools_per_category, + fill_lab_tool_section, + filter_tools, get_all_installed_tool_ids_on_server, - get_github_repo, + get_conda_package, + get_first_commit_for_local_folder, get_last_url_position, - get_suite_ID_fallback, - get_tool_github_repositories, + get_shed_attribute, + get_tool_metadata_from_local, get_tool_outputs, get_tool_stats_from_stats_file, + get_xref, + parse_tools_from_local, STATS_SUM, ) -from github import Github from requests import HTTPError SCRIPT_DIR = os.path.dirname(os.path.realpath(__file__)) @@ -180,182 +201,6 @@ def test_adds_related_workflows(self) -> None: self.assertEqual(sorted(expected_mapping[res["Suite ID"]]), sorted(res["Related Workflows"])) -class TestGetSuiteIDFallback(unittest.TestCase): - - def test_suite_id_already_set(self) -> None: - metadata: Dict[str, Any] = {"Suite ID": "existing_suite", "bio.tool ID": "SomeTool"} - tool = Mock() - tool.path = "some/path/to/tool_folder" - result = get_suite_ID_fallback(metadata, tool) - self.assertEqual(result["Suite ID"], "existing_suite") - - def test_suite_id_none_bio_tool_id_present(self) -> None: - metadata: Dict[str, Any] = {"Suite ID": None, "bio.tool ID": "MyToolSuite"} - tool = Mock() - tool.path = "some/path/to/tool_folder" - result = get_suite_ID_fallback(metadata, tool) - self.assertEqual(result["Suite ID"], "mytoolsuite") - - def test_suite_id_and_bio_tool_id_none(self) -> None: - metadata: Dict[str, Any] = {"Suite ID": None, "bio.tool ID": None} - tool = Mock() - tool.path = "toolshed/repos/dev/suite_xyz" - result = get_suite_ID_fallback(metadata, tool) - self.assertEqual(result["Suite ID"], "suite_xyz") - - -class TestGetToolGithubRepositories(unittest.TestCase): - """ - Unit tests for the get_tool_github_repositories function. - """ - - def setUp(self) -> None: - """ - Shared mock setup for GitHub repo hierarchy and content. - """ - # Mocked file content returned by get_string_content - self.mock_repositories_content: str = ( - "https://github.com/genouest/galaxy-tools\n" - "https://github.com/galaxyproject/galaxy\n" - "https://github.com/TGAC/earlham-galaxytools\n" - ) - - # Mock GitHub repo object - self.mock_content: Any = MagicMock() - self.mock_repo: Any = MagicMock() - self.mock_repo.get_contents.return_value = self.mock_content - - # Mock GitHub user - self.mock_user: Any = MagicMock() - self.mock_user.get_repo.return_value = self.mock_repo - - # Mock GitHub instance - self.mock_g: Any = MagicMock() - self.mock_g.get_user.return_value = self.mock_user - - @patch("extract_galaxy_tools.get_string_content") - def test_get_tool_github_repositories(self, mock_get_string_content: MagicMock) -> None: - """ - Test that get_tool_github_repositories returns a list of repository URLs - when run_test=False and add_extra_repositories=False. - """ - mock_get_string_content.return_value = self.mock_repositories_content - - result: list[str] = get_tool_github_repositories( - g=self.mock_g, - repository_list="repositories01.list", - run_test=False, - add_extra_repositories=False, - ) - - self.assertEqual( - result, - [ - "https://github.com/genouest/galaxy-tools", - "https://github.com/galaxyproject/galaxy", - "https://github.com/TGAC/earlham-galaxytools", - ], - ) - - self.mock_repo.get_contents.assert_called_once_with("repositories01.list") - mock_get_string_content.assert_called_once_with(self.mock_content) - - @patch("extract_galaxy_tools.configs", {"extra-repositories": ["https://github.com/extra/repo"]}) - @patch("extract_galaxy_tools.get_string_content") - def test_get_tool_github_repositories_with_extra(self, mock_get_string_content: MagicMock) -> None: - """ - Test that get_tool_github_repositories appends extra repositories from config - when add_extra_repositories=True. - """ - mock_get_string_content.return_value = self.mock_repositories_content - - result: list[str] = get_tool_github_repositories( - g=self.mock_g, - repository_list="repositories01.list", - run_test=False, - add_extra_repositories=True, - ) - - self.assertEqual( - result, - [ - "https://github.com/genouest/galaxy-tools", - "https://github.com/galaxyproject/galaxy", - "https://github.com/TGAC/earlham-galaxytools", - "https://github.com/extra/repo", - ], - ) - - -class TestGetGithubRepo(unittest.TestCase): - """ - Unit tests for the get_github_repo function. - """ - - def test_valid_repo_url(self) -> None: - """ - Test that a valid GitHub URL returns the correct mocked repository object. - """ - mock_repo = MagicMock() - mock_user = MagicMock() - mock_user.get_repo.return_value = mock_repo - - mock_g = MagicMock(spec=Github) - mock_g.get_user.return_value = mock_user - - url = "https://github.com/galaxyproject/galaxy" - result = get_github_repo(url, mock_g) - - self.assertEqual(result, mock_repo) - mock_g.get_user.assert_called_once_with("galaxyproject") - mock_user.get_repo.assert_called_once_with("galaxy") - - def test_url_with_trailing_slash(self) -> None: - """ - Test that URLs ending with a slash are handled correctly. - """ - mock_repo = MagicMock() - mock_user = MagicMock() - mock_user.get_repo.return_value = mock_repo - - mock_g = MagicMock() - mock_g.get_user.return_value = mock_user - - url = "https://github.com/usegalaxy-eu/tools-iuc/" - result = get_github_repo(url, mock_g) - - self.assertEqual(result, mock_repo) - mock_g.get_user.assert_called_once_with("usegalaxy-eu") - mock_user.get_repo.assert_called_once_with("tools-iuc") - - def test_url_with_dot_git_suffix(self) -> None: - """ - Test that URLs ending with .git are cleaned and handled. - """ - mock_repo = MagicMock() - mock_user = MagicMock() - mock_user.get_repo.return_value = mock_repo - - mock_g = MagicMock() - mock_g.get_user.return_value = mock_user - - url = "https://github.com/usegalaxy-eu/tools-iuc.git" - result = get_github_repo(url, mock_g) - - self.assertEqual(result, mock_repo) - mock_g.get_user.assert_called_once_with("usegalaxy-eu") - mock_user.get_repo.assert_called_once_with("tools-iuc") - - def test_invalid_url(self) -> None: - """ - Test that a ValueError is raised when the URL does not start with the expected prefix. - """ - mock_g = MagicMock() - - with self.assertRaises(ValueError): - get_github_repo("http://example.com/repo", mock_g) - - class TestGetLastUrlPosition(unittest.TestCase): """ Unit tests for the get_last_url_position function. @@ -406,7 +251,7 @@ def test_successful_fetch(self, mock_get: MagicMock) -> None: self.assertEqual(ids1, expected) self.assertEqual(ids2, expected) - mock_get.assert_called_with("https://usegalaxy.org/api/tools", params={"in_panel": False}) + mock_get.assert_called_with("https://usegalaxy.org/api/tools", params={"in_panel": False}, timeout=30) @patch("extract_galaxy_tools.requests.get") def test_raise_for_status_failure(self, mock_get: MagicMock) -> None: @@ -428,3 +273,574 @@ def test_json_parse_failure(self, mock_get: MagicMock) -> None: result = get_all_installed_tool_ids_on_server("https://usegalaxy.org") self.assertEqual(result, []) + + +class TestNormalizeRepoUrl(unittest.TestCase): + def test_strips_trailing_slash(self) -> None: + self.assertEqual( + _normalize_repo_url("https://github.com/iuc/tools/"), + "https://github.com/iuc/tools", + ) + + def test_strips_dot_git(self) -> None: + self.assertEqual( + _normalize_repo_url("https://github.com/iuc/tools.git"), + "https://github.com/iuc/tools", + ) + + def test_strips_both(self) -> None: + self.assertEqual( + _normalize_repo_url("https://github.com/iuc/tools.git/"), + "https://github.com/iuc/tools", + ) + + def test_strips_whitespace(self) -> None: + self.assertEqual( + _normalize_repo_url(" https://github.com/iuc/tools "), + "https://github.com/iuc/tools", + ) + + +class TestRepoNameFromUrl(unittest.TestCase): + def test_standard_github(self) -> None: + self.assertEqual( + _repo_name_from_url("https://github.com/galaxyproject/tools-iuc"), + "galaxyproject-tools-iuc", + ) + + def test_with_dot_git(self) -> None: + self.assertEqual( + _repo_name_from_url("https://github.com/iuc/fastp.git"), + "iuc-fastp", + ) + + def test_trailing_slash(self) -> None: + self.assertEqual( + _repo_name_from_url("https://github.com/bgruening/galaxytools/"), + "bgruening-galaxytools", + ) + + +class TestGetFirstCommitForLocalFolder(unittest.TestCase): + def setUp(self) -> None: + self.repo_path = Path("/fake/repo") + + @patch("extract_galaxy_tools.subprocess.run") + def test_returns_first_commit_date(self, mock_run: MagicMock) -> None: + mock_result = MagicMock() + mock_result.stdout = "2024-03-12\n2024-06-01\n" + mock_run.return_value = mock_result + + date = get_first_commit_for_local_folder(self.repo_path, "tools/fastp") + + self.assertEqual(date, "2024-03-12") + + @patch("extract_galaxy_tools.subprocess.run") + def test_empty_output_returns_empty(self, mock_run: MagicMock) -> None: + mock_result = MagicMock() + mock_result.stdout = "" + mock_run.return_value = mock_result + + date = get_first_commit_for_local_folder(self.repo_path, "tools/fastp") + + self.assertEqual(date, "") + + @patch("extract_galaxy_tools.subprocess.run") + @patch("extract_galaxy_tools.Path.exists") + def test_deepens_shallow_clone_when_empty(self, mock_exists: MagicMock, mock_run: MagicMock) -> None: + mock_exists.return_value = True # shallow file exists + + mock_run.side_effect = [ + MagicMock(stdout=""), + MagicMock(stdout="", returncode=0), + MagicMock(stdout="2020-01-15\n"), + ] + + date = get_first_commit_for_local_folder(self.repo_path, "tools/fastp") + + self.assertEqual(date, "2020-01-15") + self.assertEqual(mock_run.call_count, 3) + + @patch("extract_galaxy_tools.subprocess.run") + @patch("extract_galaxy_tools.Path.exists") + def test_does_not_deepen_when_date_found_first(self, mock_exists: MagicMock, mock_run: MagicMock) -> None: + mock_run.return_value = MagicMock(stdout="2024-03-12\n") + + date = get_first_commit_for_local_folder(self.repo_path, "tools/fastp") + + self.assertEqual(date, "2024-03-12") + self.assertEqual(mock_run.call_count, 1) + mock_exists.assert_not_called() + + +class TestGetToolMetadataFromLocalReal(unittest.TestCase): + """Tests using real Galaxy tool wrappers from the CI test repository.""" + + test_data: Path + fastp_tool: Path + threshold_tool: Path + + @classmethod + def setUpClass(cls) -> None: + cls.test_data = Path(__file__).parent / "test-data" + cls.fastp_tool = cls.test_data / "fastp_test" + cls.threshold_tool = cls.test_data / "2d_auto_threshold_test" + + @patch("extract_galaxy_tools.get_first_commit_for_local_folder") + @patch("extract_galaxy_tools.requests.get") + def test_fastp_metadata(self, mock_requests_get: MagicMock, mock_first_commit: MagicMock) -> None: + mock_first_commit.return_value = "2024-01-01" + mock_requests_get.return_value.status_code = 404 + + metadata = get_tool_metadata_from_local(self.fastp_tool, self.fastp_tool.parent, repo_url="") + + assert metadata is not None + self.assertEqual(metadata["Suite ID"], "fastp") + self.assertEqual(metadata["Suite version"], "0.23.2") + self.assertEqual(metadata["Suite owner"], "iuc") + self.assertEqual(metadata["bio.tool ID"], "fastp") + self.assertEqual(metadata["Suite conda package"], "fastp") + self.assertEqual(metadata["Tool IDs"], ["fastp"]) + self.assertIn("Sequence Analysis", metadata["ToolShed categories"]) + self.assertEqual(metadata["Homepage"], "https://github.com/OpenGene/fastp") + + @patch("extract_galaxy_tools.get_first_commit_for_local_folder") + @patch("extract_galaxy_tools.requests.get") + def test_2d_auto_threshold_metadata(self, mock_requests_get: MagicMock, mock_first_commit: MagicMock) -> None: + mock_first_commit.return_value = "2024-01-01" + mock_requests_get.return_value.status_code = 404 + + metadata = get_tool_metadata_from_local(self.threshold_tool, self.threshold_tool.parent, repo_url="") + + assert metadata is not None + self.assertEqual(metadata["Suite ID"], "2d_auto_threshold") + self.assertEqual(metadata["Suite version"], "0.0.6-2") + self.assertEqual(metadata["Suite owner"], "imgteam") + self.assertEqual(metadata["bio.tool ID"], "scikit-image") + self.assertEqual(metadata["Suite conda package"], "scikit-image") + self.assertEqual(metadata["Tool IDs"], ["ip_threshold"]) + self.assertIn("Imaging", metadata["ToolShed categories"]) + + @patch("extract_galaxy_tools.get_first_commit_for_local_folder") + @patch("extract_galaxy_tools.requests.get") + def test_parsed_folder_with_repo_url(self, mock_requests_get: MagicMock, mock_first_commit: MagicMock) -> None: + mock_first_commit.return_value = "2024-01-01" + mock_requests_get.return_value.status_code = 404 + + metadata = get_tool_metadata_from_local( + self.fastp_tool, + self.fastp_tool.parent, + repo_url="https://github.com/owner/repo", + ) + + assert metadata is not None + expected = "https://github.com/owner/repo/tree/master/fastp_test" + self.assertEqual(metadata["Suite parsed folder"], expected) + + @patch("extract_galaxy_tools.get_first_commit_for_local_folder") + @patch("extract_galaxy_tools.requests.get") + def test_parsed_folder_without_repo_url(self, mock_requests_get: MagicMock, mock_first_commit: MagicMock) -> None: + mock_first_commit.return_value = "2024-01-01" + mock_requests_get.return_value.status_code = 404 + + metadata = get_tool_metadata_from_local(self.fastp_tool, self.fastp_tool.parent, repo_url="") + + assert metadata is not None + self.assertEqual(metadata["Suite parsed folder"], str(self.fastp_tool)) + + @patch("extract_galaxy_tools.requests.get") + def test_first_commit_date_is_fetched(self, mock_requests_get: MagicMock) -> None: + """Verify the function calls get_first_commit_for_local_folder.""" + mock_requests_get.return_value.status_code = 404 + + metadata = get_tool_metadata_from_local(self.fastp_tool, self.fastp_tool.parent, repo_url="") + + assert metadata is not None + self.assertIn("Suite first commit date", metadata) + + +class TestGetShedAttribute(unittest.TestCase): + def test_returns_value_when_key_exists(self) -> None: + content = {"name": "fastp", "owner": "iuc"} + self.assertEqual(get_shed_attribute("name", content, None), "fastp") + self.assertEqual(get_shed_attribute("owner", content, None), "iuc") + + def test_returns_empty_when_key_missing(self) -> None: + content = {"name": "fastp"} + self.assertIsNone(get_shed_attribute("owner", content, None)) + self.assertEqual(get_shed_attribute("owner", content, []), []) + + +class TestGetXref(unittest.TestCase): + def setUp(self) -> None: + xml = """ + + fastp + some-biii-id + + """ + self.el = et.fromstring(xml) + + def test_finds_biotools(self) -> None: + self.assertEqual(get_xref(self.el, "bio.tools"), "fastp") + + def test_finds_biii(self) -> None: + self.assertEqual(get_xref(self.el, "biii"), "some-biii-id") + + def test_returns_none_when_type_missing(self) -> None: + self.assertIsNone(get_xref(self.el, "nonexistent")) + + def test_returns_none_when_no_xrefs(self) -> None: + el = et.fromstring("") + self.assertIsNone(get_xref(el, "bio.tools")) + + +class TestGetCondaPackage(unittest.TestCase): + def test_returns_first_requirement(self) -> None: + xml = """ + + fastp + zip + + """ + el = et.fromstring(xml) + self.assertEqual(get_conda_package(el), "fastp") + + def test_returns_none_when_no_requirements(self) -> None: + el = et.fromstring("") + self.assertIsNone(get_conda_package(el)) + + +class TestCheckCategories(unittest.TestCase): + def test_returns_true_when_intersection(self) -> None: + self.assertTrue(check_categories(["Imaging", "Sequence Analysis"], ["Imaging"])) # type: ignore[arg-type] + + def test_returns_false_when_no_intersection(self) -> None: + self.assertFalse(check_categories(["Imaging"], ["Sequence Analysis"])) # type: ignore[arg-type] + + def test_returns_true_when_filter_empty(self) -> None: + self.assertTrue(check_categories(["Imaging"], [])) # type: ignore[arg-type] + + def test_returns_false_when_tool_categories_empty(self) -> None: + self.assertFalse(check_categories([], ["Imaging"])) # type: ignore[arg-type] + + def test_returns_false_when_tool_categories_none(self) -> None: + self.assertFalse(check_categories(None, ["Imaging"])) # type: ignore[arg-type] + + +class TestAddStatus(unittest.TestCase): + def setUp(self) -> None: + self.tool = {"Suite ID": "fastp", "Suite owner": "iuc"} + + def test_sets_keep_and_deprecated_when_found(self) -> None: + status_df = pd.DataFrame( + {"Suite ID": ["fastp"], "Suite owner": ["iuc"], "To keep": [True], "Deprecated": [False]} + ) + add_status(self.tool, status_df) + self.assertTrue(self.tool["To keep"]) + self.assertFalse(self.tool["Deprecated"]) + + def test_sets_none_when_not_found(self) -> None: + status_df = pd.DataFrame(columns=["Suite ID", "Suite owner", "To keep", "Deprecated"]) + add_status(self.tool, status_df) + self.assertIsNone(self.tool["To keep"]) + self.assertIsNone(self.tool["Deprecated"]) + + def test_handles_missing_owner_column(self) -> None: + status_df = pd.DataFrame({"Suite ID": ["fastp"], "To keep": [True], "Deprecated": [False]}) + add_status(self.tool, status_df) + self.assertTrue(self.tool["To keep"]) + + +class TestFilterTools(unittest.TestCase): + def test_filters_by_category_and_adds_status(self) -> None: + tools = [ + {"ToolShed categories": ["Imaging"], "Suite ID": "t1", "Suite owner": "o1"}, + {"ToolShed categories": ["Sequence Analysis"], "Suite ID": "t2", "Suite owner": "o2"}, + ] + status_df = pd.DataFrame({"Suite ID": ["t1"], "Suite owner": ["o1"], "To keep": [True], "Deprecated": [False]}) + result = filter_tools(tools, ["Imaging"], status_df) + self.assertEqual(len(result), 1) + self.assertEqual(result[0]["Suite ID"], "t1") + self.assertTrue(result[0]["To keep"]) + + +class TestCurateTools(unittest.TestCase): + def setUp(self) -> None: + status_df = pd.DataFrame( + { + "Suite ID": ["t1", "t2"], + "Suite owner": ["o1", "o2"], + "To keep": [True, True], + "Deprecated": [False, False], + } + ) + self.tools: List[Dict[str, Any]] = [ + {"Suite ID": "t1", "Suite owner": "o1", "bio.tool ID": "fastp"}, + {"Suite ID": "t2", "Suite owner": "o2", "bio.tool ID": None}, + {"Suite ID": "t3", "Suite owner": "o3", "bio.tool ID": "other"}, + ] + self.curated, self.without, self.with_ = curate_tools(self.tools, status_df) + + def test_returns_only_keep_tools(self) -> None: + self.assertEqual(len(self.curated), 2) + + def test_splits_by_biotools(self) -> None: + self.assertEqual(len(self.without), 1) + self.assertEqual(len(self.with_), 1) + + def test_adds_status_to_all(self) -> None: + for t in self.curated: + self.assertIn("To keep", t) + + +class TestExportToolsToJson(unittest.TestCase): + def test_writes_json_file(self) -> None: + tools = [{"Suite ID": "fastp", "Suite version": "1.0"}] + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".json") + tmp.close() + try: + export_tools_to_json(tools, tmp.name) + with open(tmp.name) as f: + data = json.load(f) + self.assertEqual(data, tools) + finally: + os.remove(tmp.name) + + +class TestExportToolsToTsv(unittest.TestCase): + def test_writes_tsv_file(self) -> None: + tools = [{"Suite ID": "fastp", "Suite version": "1.0"}] + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".tsv") + tmp.close() + try: + export_tools_to_tsv(tools, tmp.name) + df = pd.read_csv(tmp.name, sep="\t") + self.assertEqual(df.iloc[0]["Suite ID"], "fastp") + finally: + os.remove(tmp.name) + + def test_formats_list_columns(self) -> None: + tools = [ + { + "Suite ID": "fastp", + "ToolShed categories": ["Imaging", "Sequence Analysis"], + "EDAM operations": [], + "EDAM topics": [], + "EDAM reduced operations": [], + "EDAM reduced topics": [], + "Related Workflows": [], + "Related Tutorials": [], + "Tool IDs": [], + "Tool output formats": [], + } + ] + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".tsv") + tmp.close() + try: + export_tools_to_tsv(tools, tmp.name, format_list_col=True) + df = pd.read_csv(tmp.name, sep="\t") + self.assertIn("Imaging, Sequence Analysis", df.iloc[0]["ToolShed categories"]) + finally: + os.remove(tmp.name) + + +class TestExportToolsToYml(unittest.TestCase): + @patch("extract_galaxy_tools.shared.export_to_yml") + def test_calls_shared_export(self, mock_export: MagicMock) -> None: + tools = [{"Suite ID": "fastp"}] + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".yml") + tmp.close() + try: + export_tools_to_yml(tools, tmp.name) + mock_export.assert_called_once() + finally: + os.remove(tmp.name) + + +class TestCheckToolsOnServers(unittest.TestCase): + @patch("extract_galaxy_tools.get_all_installed_tool_ids_on_server") + def test_counts_matching_tools(self, mock_get_ids: MagicMock) -> None: + mock_get_ids.return_value = [ + "toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/1.0", + "toolshed.g2.bx.psu.edu/repos/iuc/snpsift/snpSift_filter/2.0", + ] + count = check_tools_on_servers(["fastp", "nonexistent"], "https://usegalaxy.org") + self.assertEqual(count, 1) + + @patch("extract_galaxy_tools.get_all_installed_tool_ids_on_server") + def test_works_with_short_ids(self, mock_get_ids: MagicMock) -> None: + mock_get_ids.return_value = ["fastp", "snpSift_filter"] + count = check_tools_on_servers(["fastp"], "https://usegalaxy.org") + self.assertEqual(count, 1) + + +class TestCloneRepositories(unittest.TestCase): + @patch("extract_galaxy_tools.subprocess.run") + def test_clones_new_repositories(self, mock_run: MagicMock) -> None: + with tempfile.TemporaryDirectory() as tmp: + clone_dir = Path(tmp) / "clones" + result = clone_repositories( + ["https://github.com/iuc/fastp"], + clone_dir, + depth=1, + ) + self.assertEqual(len(result), 1) + self.assertEqual(result[0][0], "https://github.com/iuc/fastp") + self.assertTrue(result[0][1].name, "iuc-fastp") + mock_run.assert_called() + + @patch("extract_galaxy_tools.subprocess.run") + def test_skips_duplicates(self, mock_run: MagicMock) -> None: + with tempfile.TemporaryDirectory() as tmp: + clone_dir = Path(tmp) / "clones" + result = clone_repositories( + ["https://github.com/iuc/fastp", "https://github.com/iuc/fastp"], + clone_dir, + depth=1, + ) + self.assertEqual(len(result), 1) + + +class TestParseToolsFromLocal(unittest.TestCase): + def setUp(self) -> None: + self.tmp = tempfile.TemporaryDirectory() + self.repo_path = Path(self.tmp.name) / "repo" + tools_dir = self.repo_path / "tools" + tools_dir.mkdir(parents=True) + # copy the fastp_test wrapper as a tool subdir + src = Path(__file__).parent / "test-data" / "fastp_test" + dest = tools_dir / "fastp" + shutil.copytree(src, dest) + + def tearDown(self) -> None: + self.tmp.cleanup() + + @patch("extract_galaxy_tools.get_first_commit_for_local_folder") + @patch("extract_galaxy_tools.requests.get") + def test_parses_tools_from_local_repo(self, mock_requests_get: MagicMock, mock_first_commit: MagicMock) -> None: + mock_first_commit.return_value = "2024-01-01" + mock_requests_get.return_value.status_code = 404 + tools = parse_tools_from_local(self.repo_path, workers=1) + self.assertEqual(len(tools), 1) + self.assertEqual(tools[0]["Suite ID"], "fastp") + + +class TestExtractTopToolsPerCategory(unittest.TestCase): + def test_returns_top_tools(self) -> None: + data = { + "Suite ID": [f"tool{i}" for i in range(12)], + "EDAM operations": (["Quality control"] * 6) + (["Alignment"] * 6), + "Suite runs on main servers": list(range(100, 112)), + } + df = pd.DataFrame(data) + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".tsv") + tmp.close() + try: + df.to_csv(tmp.name, sep="\t", index=False) + result = extract_top_tools_per_category( + tmp.name, count_column="Suite runs on main servers", category_nb=10, top_tool_nb=5 + ) + self.assertIsInstance(result, pd.DataFrame) + self.assertGreater(len(result), 0) + self.assertIn("Category", result.columns) + finally: + os.remove(tmp.name) + + +class TestFillLabToolSection(unittest.TestCase): + def test_fills_section(self) -> None: + lab_section = {"id": "lab", "title": "Lab", "tabs": [{"id": "more_tools"}]} + data = { + "Suite ID": ["fastp"], + "Category": ["Quality control"], + "Description": ["Fast preprocessor"], + "Tool IDs": ["fastp"], + "Suite runs on main servers": [100], + } + df = pd.DataFrame(data) + result = fill_lab_tool_section(lab_section, df) + self.assertEqual(result["id"], "lab") + self.assertGreater(len(result["tabs"]), 0) + self.assertEqual(result["tabs"][0]["id"], "more_tools") + + +class TestExportMissingToolsToYaml(unittest.TestCase): + def test_writes_yaml(self) -> None: + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".yaml") + tmp.close() + try: + export_missing_tools_to_yaml( + Path(tmp.name), [{"name": "fastp", "owner": "iuc", "tool_panel_section_id": ""}] + ) + with open(tmp.name) as f: + content = yaml.safe_load(f) + self.assertIn("tools", content) + self.assertEqual(len(content["tools"]), 1) + finally: + os.remove(tmp.name) + + +class TestExportMissingTools(unittest.TestCase): + def test_creates_all_and_top_dirs(self) -> None: + missing = {"Server1": {"all": [{"name": "fastp", "owner": "iuc", "tool_panel_section_id": ""}], "top": []}} + with tempfile.TemporaryDirectory() as tmp: + export_missing_tools(missing, tmp) + all_dir = Path(tmp) / "all" + top_dir = Path(tmp) / "top" + self.assertTrue(all_dir.is_dir()) + self.assertTrue(top_dir.is_dir()) + + def test_sanitizes_server_names(self) -> None: + missing = { + "UseGalaxy.org (Main)": {"all": [], "top": [{"name": "fastp", "owner": "iuc", "tool_panel_section_id": ""}]} + } + with tempfile.TemporaryDirectory() as tmp: + export_missing_tools(missing, tmp) + top_dir = Path(tmp) / "top" + found = list(top_dir.iterdir()) + self.assertEqual(len(found), 1) + # parens and spaces replaced + self.assertNotIn("(", found[0].name) + + +class TestLoadToolXmlFallback(unittest.TestCase): + def test_parses_valid_xml(self) -> None: + xml_path = Path(__file__).parent / "test-data" / "fastp_test" / "fastp.xml" + tree = _load_tool_xml_fallback(xml_path) + assert tree is not None + root = tree.getroot() + self.assertEqual(root.attrib["id"], "fastp") + + def test_returns_none_on_invalid_xml(self) -> None: + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".xml", mode="w") + tmp.write("not valid xml") + tmp.close() + try: + result = _load_tool_xml_fallback(Path(tmp.name)) + self.assertIsNone(result) + finally: + os.remove(tmp.name) + + +class TestExtractMissingToolsPerServers(unittest.TestCase): + def test_returns_missing_tools_dict(self) -> None: + data = { + "Suite ID": [f"tool{i}" for i in range(12)], + "EDAM operations": (["Quality control"] * 6) + (["Alignment"] * 6), + "Suite runs on main servers": list(range(100, 112)), + "Tool IDs": [f"tool{i}" for i in range(12)], + "Suite owner": ["iuc"] * 12, + "Number of tools on UseGalaxy.eu": [1] * 12, + } + df = pd.DataFrame(data) + tmp = tempfile.NamedTemporaryFile(delete=False, suffix=".tsv") + tmp.close() + try: + df.to_csv(tmp.name, sep="\t", index=False) + result = extract_missing_tools_per_servers(tmp.name) + self.assertIsInstance(result, dict) + self.assertIn("Local_Galaxy", result) + self.assertIn("all", result["Local_Galaxy"]) + finally: + os.remove(tmp.name) diff --git a/sources/bin/tests/test_extract_galaxy_workflows.py b/sources/bin/tests/test_extract_galaxy_workflows.py index 451c16a71..3888146eb 100644 --- a/sources/bin/tests/test_extract_galaxy_workflows.py +++ b/sources/bin/tests/test_extract_galaxy_workflows.py @@ -1,5 +1,6 @@ import json import os +import sys import unittest from typing import Dict from unittest.mock import ( @@ -7,8 +8,10 @@ patch, ) -from bin import shared -from bin.extract_galaxy_workflows import Workflows +sys.path.insert(0, os.path.join(os.path.dirname(__file__), "..")) + +import shared +from extract_galaxy_workflows import Workflows class TestAddWorkflowsFromWorkflowHub(unittest.TestCase):