labgem/pan2met-wf is a bioinformatics pipeline that predicts metabolic network of procaryotes at pangenome scale. It takes, either a set of genomes, a PPanGGOLiN pangenome, or directly a proteome in FASTA format and predict what metabolic pathways forms the metabolism of the organism.
A typical workflow boils down into these main steps:
- Prepare a PPanGGOLiN pangenome (PPanGGOLiN)
- Identify reference proteins for gene families (PPanGGOLiN)
- Align MetaCyc proteins with the gene families reference proteins (diamond blastp); associate the found homolog proteins with MetaCyc reaction identifiers.
- Align EcoCyc proteins with the gene families reference proteins (diamond blastp); associate the found homolog proteins with MetaCyc reaction identifiers.
- Scan the gene families reference proteins for KEGG KOFam (KOFamScan); associate the KEGG KO identified, with MetaCyc reaction identifiers, or, if none found, EC-numbers.
- Merge EcoCyc-, MetaCyc- and KOFam-based MetaCyc reaction identifiers annotations. Keep at first, the EcoCyc-based annotation. If none found, keep the MetaCyc-based annotation. Again, if none found, keep the MetaCyc reaction identifiers obtained through KOFamScan. In last resort, if no MetaCyc reaction identifier could be found, and there exist a EC-number associated with the protein, keep this EC-number.7
Note
If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.
Now, you can run the pipeline using:
nextflow run labgem/pan2met-wf \
-profile <docker/singularity/.../institute> \
--input samplesheet.csv \
--outdir <OUTDIR>Warning
Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.
labgem/pan2met-wf was originally written by Samuel Ortion.
We thank the following people for their extensive assistance in the development of this pipeline:
If you would like to contribute to this pipeline, please see the contributing guidelines.
An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.