scoary

Tags: scoary pangenome gwas association bacteria roary run-scope

Pan-genome wide association studies.

Uses Scoary to score the components of the pan-genome for associations to specified traits (phenotypes). It is designed to work with the gene presence/absence output from Roary.

Inputs

record (
    meta: Record,
    csv: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
csv	Path	Gene presence/absence CSV file (typically from Roary)

traits: Path

Name	Type	Description
traits	Path	CSV file containing trait information for the samples

Outputs

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

Field	Type	Description
meta	Record	Sample information record
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

Scoary Parameters

Parameter	Type	Default	Description
--scoary_traits	string		Input trait table (CSV) to test for associations
--scoary_permute	integer	0	Perform N number of permutations of the significant results post-analysis

Used By

Subworkflows

• scoary - Pan-genome wide association studies.

Workflows

• pangenome - Pangenome analysis with optional core-genome phylogeny.

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)

• Scoary
  Brynildsrud O, Bohlin J, Scheffer L, Eldholm V Rapid scoring of genes in microbial pan-genome-wide association studies with Scoary. Genome Biol. 17:238 (2016)

Source

View source on GitHub

Version

SCOARY:
    - scoary: 1.6.16