Readme.md

MetaCoCo: METAbolism COmpletion for microbial COmmunities

MetaCoCo is a Bash/Python pipeline that generates a completion matrix of MetaCyc metabolic pathways for one or multiple bacterial genomes or metagenomes, starting from FASTA files.

The pipeline performs:

• gene prediction using Prodigal,
• functional annotation with KofamScan,
• metabolic pathway inference using Pathway Tools.

This version is currently designed to run MetaCoCo on a Linux cluster using the SLURM job scheduler and Environment Modules for managing the following software dependencies:

Usage

• Run the main script:

sbatch --array=0-N run_ptools_pipeline.sh -i GENOMES/ -o results -f metacoco_input.csv -t HIGH/MIDDLE/LOW
or 
sbatch --array=0-N run_ptools_pipeline.sh -i GENOMES/ -o results -f metacoco_input.csv -t HIGH/MIDDLE/LOW -p ANNOTATIONS/

• Once it's done, please run:

sbatch -c2 run_create_completion_matrix.sh -i results/ -l results/Shortname.txt

Input files

The script takes a folder containing fasta files, an metacoco_input.csv file and a -t argument to specify the threshold of stringency, as input.

A optional argument -p allow to give your own annotations.

Input data

Folder_input

metacoco_input.csv

GENOMES/

├── GENOME1_genomic.fna

├── GENOME2_genomic.fna

├── GENOME3_genomic.fna

│   ...

Input files must have the exact same name as in the metacoco_input.csv and finished with _genomic.fna

WARNING

As Pathway Tools is very specific about names, please use only name in uppercase and without any other specific character

ex : gca_XXXX_genomic.fna

=> GCAXXXX_genomic.fna

metacoco_input.csv file

This is a required file to run PathoLogic and allowed to give more informations to Pathway Tools. The more precise you are, the more accurate will be the prediction.

This is a tabulated file, with minimum informations as followed :

| ncbi_organism_name | ncbi_strain_identifiers | ncbi_taxid |

| GENOME1 | GCAXXXXX |  1735114 |

| GENOME2 | GCAXXXXX |  1926873 |

Output files

MetaCoCo is going to produce two types of completion matrix:

• Individual matrix for each genome

• 1 matrix gathering all the results of each genome

In the results/ folder you will find the raw results of Pathologic/Pathway Tools.

For more informations about the differents formats, please refer here: https://bioinformatics.ai.sri.com/ptools/flatfile-format.html

In your main folder you will find all the matrix in a csv tabulated format.

References

.. [Hyatt2010] Hyatt, D., Chen, G.-L., Locascio, P. F., Land, M. L., Larimer, F. W. & Hauser, L. J. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010). https://doi.org/10.1186/1471-2105-11-119

.. [Aramaki2020] Aramaki, T., Blanc-Mathieu, R., Endo, H., Ohkubo, K., Kanehisa, M., Goto, S. & Ogata, H. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36(7), 2251–2252 (2020). https://doi.org/10.1093/bioinformatics/btz859

... [MetaCyc20] R.Caspi, R.Billington, I.M. Keseler, A.Kothari, M.Krummenacker, P.E.Midford, W.K. Ong, S.Paley, P.Subhraveti, P.D. Karp The MetaCyc database of metabolic pathways and enzymes - a 2019 update Nucleic Acids Res48(D1):D445-D453 (2020). https://doi.org/10.1093/nar/gkz862

.. [PTools24] Karp, P. D., Paley, S. M., Midford, P. E., Krummenacker, M., Billington, R., Kothari, A., Ong, W. K., Subhraveti, P., Keseler, I. M. & Caspi R. Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology. arXiv (2024). https://doi.org/10.48550/arXiv.1510.03964

License

This software is licensed under the GNU Lesser General Public License v3.0