Codes used in the ChloroScan benchmarking and data preparations.
- Bash commands used in generating synthetic metagenomes and benchmarking ChloroScan:
codes/bash_codes.md. Codes such as downloading NCBI dataset genomes, running binning benchmarking and running binning tools (MetaBAT2/ChloroScan) are here.
Note: ChloroScan v0.1.5 is used here for generating these results, the command to download is: pip install chloroscan==0.1.5.
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Codes used in generating marker gene database:
codes/marker_gene_database_commands.md. -
OrthoFinder outputs and the scripts and files involved in generating the marker gene database are dumped here: https://doi.org/10.26188/28722788. A copy of result files and intermediary files for generating marker gene database is in
marker_gene_database_complete.tar.gz. Before running codes in./codes/marker_gene_database_commands.md, please download the files from figshare. The command to download is:
wget --referer=https://figshare.unimelb.edu.au --user-agent="Mozilla/5.0" -O "marker_gene_database_complete.tar.gz" https://figshare.unimelb.edu.au/ndownloader/files/57355894