sccmec
Tags: sccmec staphylococcus-aureus mrsa antimicrobial-resistance typing sample-scope
Identify SCCmec elements in Staphylococcus aureus genomes.
This subworkflow uses SCCmec to identify the Staphylococcal Cassette Chromosome mec (SCCmec) element in Staphylococcus aureus assemblies. It predicts the type based on the presence of specific mec and ccr gene complexes, generating detailed BLAST results and typing information.
Take
assembly: Channel<Record>
| Field | Description |
|---|---|
meta | Groovy Record containing sample information |
assembly | Assembled contigs in FASTA format |
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 | Main results file with SCCmec typing |
targets | BLAST results for target sequences |
target_details | Detailed results for target matches |
regions | BLAST results for SCCmec regions |
regions_details | Detailed results for SCCmec region matches |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- sccmec - Identify SCCmec elements in Staphylococcus aureus genomes.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
Used By
This subworkflow is used by the following workflows:
- sccmec - Typing of SCCmec cassettes in 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) -
sccmec
Petit III RA, Read TD sccmec: A tool for typing SCCmec cassettes in assemblies (GitHub)