agrvate

Tags: bacteria assembly fasta typing virulence staphylococcus aureus agr sample-scope

Determine the agr locus type and operon variants in Staphylococcus aureus.

Uses AgrVATE to type the accessory gene regulator (agr) locus, a quorum sensing system critical for Staphylococcus aureus virulence.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled Staphylococcus aureus contigs in FASTA format

Outputs

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

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Tab-delimited summary of agr locus type and operon variants
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

AgrVATE Parameters

Parameter	Type	Default	Description
--agrvate_typing_only	boolean	false	agr typing only. Skips agr operon extraction and frameshift detection

Used By

Subworkflows

• agrvate - Identify Staphylococcus aureus agr locus type and operon variants.

Workflows

• agrvate - Rapid identification of Staphylococcus aureus agr locus type and agr operon variants.

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)

• AgrVATE
  Raghuram V. AgrVATE: Rapid identification of Staphylococcus aureus agr locus type and agr operon variants. (GitHub)

Source

View source on GitHub

Version

AGRVATE:
    - agrvate: 1.0.2