agrvate
Tags: staphylococcus-aureus assembly agr-locus virulence quorum-sensing sample-scope
Identify Staphylococcus aureus agr locus type and operon variants.
This subworkflow uses AgrVATE to rapidly identify the accessory gene regulator (agr) locus type and detect agr operon variants in Staphylococcus aureus. The agr system is a key quorum-sensing regulator of virulence in S. aureus.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format for agr locus detection |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
| Output | Description |
|---|---|
summary | Tab-delimited summary of agr locus type and operon variants |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- agrvate - Determine the agr locus type and operon variants in Staphylococcus aureus.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following 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)