PanGBank is a bioinformatics pipeline that uses PPanGGOLiN to generate pangenomes from a list of input genomes and taxonomy. It then prepares files for the PanGBank API.
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.
PanGBank requires two input files:
-
--genomes <genome_file_list>A TSV file with two columns:- Column 1:
Genome_name(unique name for each genome) - Column 2: Path to the corresponding genome file
- Column 1:
-
--taxonomy <genome_taxonomy>A TSV file with two columns:- Column 1:
Genome_name(must match the genome names in the--genomesfile) - Column 2: Taxonomy, a list of taxon levels separated by a semicolon (
;). The last taxon name is considered the species, and genomes will be grouped into species groups for pangenome analysis.
- Column 1:
Now, you can run the pipeline using:
nextflow run labgem/pangbank \
-profile <docker/singularity/.../institute> \
--genomes <genome_file_list> \
--taxonomy <genome_taxonomy>
--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.
PanGBank was originally written in Snakemake and has been rewritten in Nextflow by Jean Mainguy.
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.