staphopiasccmec

Tags: staphylococcus-aureus sccmec typing mrsa primers sample-scope

Primer based SCCmec typing of S. aureus genomes.

Uses Staphopia SCCmec to determine the SCCmec type of Staphylococcus aureus assemblies. It includes a primer-based approach to identify SCCmec types I-XI.

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,
    results: Set<Path>,
    logs: Set<Path?>,
    nf_logs: Set<Path>,
    versions: Set<Path>
)

Field	Type	Description
meta	Record	Sample information record
tsv	Path	TSV file with SCCmec typing results
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

Staphopia SCCmec Parameters

Parameter	Type	Default	Description
--staphopiasccmec_hamming	boolean	false	Report the results as hamming distances

Used By

Subworkflows

• staphopiasccmec - Identify SCCmec elements in Staphylococcus aureus genomes using Staphopia method.

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)

Source

View source on GitHub

Version

STAPHOPIASCCMEC:
    - staphopia-sccmec: 1.0.0