spatyper
Tags: staphylococcus-aureus spa-typing protein-a mrsa sample-scope
Predict spa types of Staphylococcus aureus from genome assemblies.
This subworkflow uses spaTyper to predict the spa types of Staphylococcus aureus strains from assembled genomes based on the polymorphic X region of the protein A gene (spa). It processes each sample individually and aggregates the results into a single consolidated report.
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 custom repeats database for spa typing |
repeat_order | Path? | Optional custom repeat order file for 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
| Output | Description |
|---|---|
tsv | spa typing results in TSV format |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
- spatyper - Finding spa types in Staphylococcus aureus.
Used By
This subworkflow is used by the following workflows:
- spatyper - spa typing of Staphylococcus aureus assemblies.
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) -
spaTyper
Sanchez-Herrero JF, and Sullivan M spaTyper: Staphylococcal protein A (spa) characterization pipeline. Zenodo. (2020)