pirate

Tags: pan-genome orthologs core-genome gene-presence-absence epidemiology annotation run-scope

Pangenome Identification and Reconciliation Analysis Tool for Epidemiology (PIRATE).

Uses PIRATE to construct the pangenome of a collection of bacterial isolates. It clusters orthologous genes and generates the core genome alignment and a gene presence/absence matrix, which is compatible with downstream analysis tools like Scoary for association testing.

Inputs

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

Field	Type	Description
meta	Record	Groovy Record containing sample information
gff	Set<Path>	A list of annotated genome files in GFF3 format

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?	The core-genome alignment (*core-genome.aln.gz), suitable for phylogenetic tree building
csv	Path?	Gene presence/absence matrix in CSV format, compatible with Scoary
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

PIRATE Parameters

Parameter	Type	Default	Description
--use_pirate	boolean	false	Use PIRATE instead of panaroo in the 'pangenome' subworkflow
--pirate_steps	string	50,60,70,80,90,95,98	Percent identity thresholds to use for pangenome construction
--pirate_features	string	CDS	Comma-delimited features to use for pangenome construction
--pirate_para_off	boolean	false	Switch off paralog identification

Used By

Subworkflows

• pirate - Build a pangenome from GFF3 annotations using PIRATE.

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)

• PIRATE
  Bayliss SC, Thorpe HA, Coyle NM, Sheppard SK, Feil EJ PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. Gigascience 8 (2019)

Source

View source on GitHub

Version

PIRATE:
    - pirate: 1.0.5