roary

Tags: pangenome orthology core-genome alignment bacteria run-scope

Rapid large-scale prokaryote pan genome analysis.

Uses Roary to calculate the pan genome of a collection of prokaryotic annotated assemblies. It outputs a core gene alignment and a gene presence/absence table.

Inputs

record (
    meta: Record,
    gff: Set<Path>
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
gff	Set<Path>	List of GFF3 files to be analyzed (typically from Prokka)

Outputs

record (
    meta: Record,
    aln: Path?,
    csv: Path?,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
aln	Path?	Core genome alignment in FASTA format
csv	Path?	Gene presence/absence table
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

Roary Parameters

Parameter	Type	Default	Description
--use_roary	boolean	false	Use Roary instead of PIRATE in the 'pangenome' subworkflow
--roary_cd	integer	99	Percentage of isolates a gene must be in to be core
--roary_s	boolean	false	Do not split paralogs
--roary_ap	boolean	false	Allow paralogs in core alignment

Used By

Subworkflows

• roary - Build a pangenome from GFF3 annotations using Roary.

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)

Source

View source on GitHub

Version

ROARY:
    - roary: 3.13.0