staphtyper
Tags: staphylococcus-aureus agr-typing spa-typing sccmec strain-characterization run-scope
Determine the agr, spa and SCCmec types for Staphylococcus aureus genomes.
This subworkflow performs comprehensive typing of Staphylococcus aureus genomes by determining the agr locus type using AgrVATE, spa repeat type using spaTyper, and SCCmec element type using SCCmec typing. It combines results from multiple typing methods to provide a complete characterization of S. aureus strains.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
repeats: Path?
repeat_order: Path?
| Name | Type | Description |
|---|---|---|
repeats | Path? | Optional spa repeats database for improved spa typing |
repeat_order | Path? | Optional spa repeat order file for improved spa typing |
Emit
Published
The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.
sample_outputs
No sample-scope outputs.
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Subworkflow Composition
This subworkflow calls the following subworkflows:
- agrvate - Identify Staphylococcus aureus agr locus type and operon variants.
- spatyper - Predict spa types of Staphylococcus aureus from genome assemblies.
- sccmec - Identify SCCmec elements in Staphylococcus aureus genomes.
Used By
This subworkflow is used by the following workflows:
- staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.
- staphtyper - Comprehensive typing of Staphylococcus aureus genomes.
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) -
spaTyper
Sanchez-Herrero JF, and Sullivan M spaTyper: Staphylococcal protein A (spa) characterization pipeline. Zenodo. (2020) -
sccmec
Petit III RA, Read TD sccmec: A tool for typing SCCmec cassettes in assemblies (GitHub)