staphopiasccmec
Tags: sccmec staphylococcus-aureus mrsa antimicrobial-resistance typing sample-scope
Identify SCCmec elements in Staphylococcus aureus genomes using Staphopia method.
This subworkflow uses staphopia-sccmec to identify Staphylococcal Cassette Chromosome mec (SCCmec) elements in Staphylococcus aureus assemblies. This is the standalone version of the SCCmec typing method developed for the Staphopia project, which predicts SCCmec types based on the presence of specific mec and ccr gene complexes.
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 | TSV file with SCCmec typing results |
run_outputs
| Output | Description |
|---|---|
csv | Aggregated results in CSV format |
Module Composition
This subworkflow calls the following modules:
- staphopiasccmec - Primer based SCCmec typing of S. aureus genomes.
- csvtk_concat - Concatenate multiple CSV or TSV files into a single table.
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) -
staphopia-sccmec
Petit III RA, Read TD Staphylococcus aureus viewed from the perspective of 40,000+ genomes. PeerJ 6, e5261 (2018)