sccmec

Tags: sccmec staphylococcus-aureus mrsa antimicrobial-resistance typing sample-scope

Identify SCCmec elements in Staphylococcus aureus genomes.

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.

Inputs

record (
    meta: Record,
    fna: Path
)

Field	Type	Description
meta	Record	Groovy Record containing sample information
fna	Path	Assembled contigs in FASTA format

Outputs

record (
    meta: Record,
    tsv: Path,
    targets: Path,
    target_details: Path,
    regions: Path,
    regions_details: Path,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	Main results file with SCCmec typing
targets	Path	BLAST results for target sequences
target_details	Path	Detailed results for target matches
regions	Path	BLAST results for SCCmec regions
regions_details	Path	Detailed results for SCCmec region matches
results	Set<Path>	All output files to be published
logs	Set<Path?>	Optional program specific log files
nf_logs	Set<Path>	Nextflow-specific log files (e.g. .command.{begin
versions	Set<Path>	A YAML formatted file with program versions

Parameters

sccmec Parameters

Parameter	Type	Default	Description
--sccmec_min_targets_pident	integer	90	Minimum percent identity to count a target hit
--sccmec_min_targets_coverage	integer	80	Minimum percent coverage to count a target hit
--sccmec_min_regions_pident	integer	85	Minimum percent identity to count a region hit
--sccmec_min_regions_coverage	integer	93	Minimum percent coverage to count a region hit

Used By

Subworkflows

• sccmec - Identify SCCmec elements in Staphylococcus aureus genomes.

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)

Source

View source on GitHub

Version

SCCMEC:
    - sccmec: 1.2.0