spatyper

Tags: staphylococcus-aureus spa-typing repeat mrsa typing sample-scope

Finding spa types in Staphylococcus aureus.

Uses spaTyper to determine the spa type of Staphylococcus aureus genomes by identifying the repeats in the polymorphic X region of the protein A gene (spa).

Inputs

record (
    meta: Record,
    fna: Path
)

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

repeats: Path?
repeat_order: Path?

Name	Type	Description
repeats	Path?	Custom repeat sequences file
repeat_order	Path?	Custom repeat order file

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	spa typing results in TSV format
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

spaTyper Parameters

Parameter	Type	Default	Description
--spatyper_repeats	string	-	List of spa repeats
--spatyper_repeat_order	string	-	List spa types and order of repeats
--spatyper_do_enrich	boolean	false	Do PCR product enrichment

Used By

Subworkflows

• spatyper - Predict spa types of Staphylococcus aureus from genome assemblies.

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)

• spaTyper Database
  Harmsen D, Claus H, Witte W, Rothgänger J, Claus H, Turnwald D, and Vogel U Typing of methicillin-resistant Staphylococcus aureus in a university hospital setting using a novel software for spa-repeat determination and database management. J. Clin. Microbiol. 41:5442-5448 (2003)

Source

View source on GitHub

Version

SPATYPER:
    - spatyper: 0.3.3