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staphtyper

Tags: staphylococcus-aureus agr-typing spa-typing sccmec surveillance strain-characterization run-scope

Determine the agr, spa, SCCmec types and perform genome-based surveillance for Staphylococcus aureus genomes.

This subworkflow performs comprehensive typing of Staphylococcus aureus genomes by determining the agr locus type using AgrVATE, spa repeat type using spaTyper, SCCmec element type using SCCmec typing, and genome-based surveillance using StaphSCAN. It combines results from multiple typing and surveillance methods to provide a complete characterization of S. aureus strains.

Take​

assembly: Channel<Record>
FieldDescription
metaGroovy Record containing sample information
assemblyAssembled contigs in FASTA format
repeats: Path?
repeat_order: Path?
staphscan_db_mlst: Path?
NameTypeDescription
repeatsPath?Optional spa repeats database for improved spa typing
repeat_orderPath?Optional spa repeat order file for improved spa typing
staphscan_db_mlstPath?Custom MLST database directory for StaphSCAN (optional)

Emit​

Published​

The sample_outputs and run_outputs emissions are aggregates of output files that will be published in the entry workflow.

sample_outputs​

No sample-scope outputs.

run_outputs​

OutputDescription
csvAggregated results in CSV format

Subworkflow Composition​

This subworkflow calls the following subworkflows:

  • agrvate - Identify Staphylococcus aureus agr locus type and operon variants.
  • sccmec - Identify SCCmec elements in Staphylococcus aureus genomes.
  • spatyper - Predict spa types of Staphylococcus aureus from genome assemblies.
  • staphscan - Genome-based surveillance analysis of Staphylococcus aureus.

Used By​

This subworkflow is used by the following workflows:

  • staphopia - Comprehensive analysis pipeline for Staphylococcus aureus isolates.
  • staphtyper - Comprehensive typing of Staphylococcus aureus genomes.

Citations​

If you use this in your analysis, please cite the following.

Source​

View source on GitHub