roary
Tags: pangenome pan-genome comparative-genomics core-genome alignment run-scope
Build a pangenome from GFF3 annotations using Roary.
This subworkflow creates a pangenome from bacterial genome annotations using Roary. Roary is a rapid pangenome pipeline that processes large numbers of annotated genomes to produce gene presence/absence matrices and core-genome alignments. It is particularly optimized for bacterial datasets and can handle hundreds of genomes efficiently.
Take
gff: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
gff | Set of GFF3 annotation files representing the genomic annotations for each sample |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
aln | Core genome alignment in FASTA format (optional) |
csv | Gene presence/absence table |
supplemental | Supplemental files including accessory binary genes and graphs |
Module Composition
This subworkflow calls the following modules:
- roary - Rapid large-scale prokaryote pan genome analysis.
Citations
If you use this in your analysis, please cite the following.
-
Bactopia
Petit III RA, Read TD Bactopia - a flexible pipeline for complete analysis of bacterial genomes. mSystems 5 (2020) -
Roary
Page AJ, Cummins CA, Hunt M, Wong VK, Reuter S, Holden MTG, Fookes M, Falush D, Keane JA, Parkhill J Roary: rapid large-scale prokaryote pan genome analysis. Bioinformatics 31, 3691-3693 (2015)