SCCmec Galaxy Wrapper

This repository contains a Galaxy wrapper for SCCmec.

SCCmec performs SCCmec typing from genome assembly FASTA files.

Command

The wrapper runs:

sccmec --input input.fasta --prefix sccmec --outdir sccmec_out --force

The filtering thresholds are exposed as advanced Galaxy options:

--min-targets-pident 90
--min-targets-coverage 80
--min-regions-pident 85
--min-regions-coverage 83

Input

Input	Format	Description
Genome assembly	FASTA	Genome assembly FASTA, intended for Staphylococcus aureus assemblies

Outputs

Output	Format	Description
Final typing	TSV	Final SCCmec type prediction
Target details	TSV	Target-based results against each type
Target BLASTN hits	TSV	Target-based BLASTN results
Region details	TSV	Region-based results against each type
Region BLASTN hits	TSV	Region-based BLASTN results
Version	TXT	SCCmec version

Database/reference files

The Bioconda package includes the SCCmec reference files under the conda environment, for example:

$CONDA_PREFIX/share/sccmec/sccmec-targets.yaml
$CONDA_PREFIX/share/sccmec/sccmec-regions.yaml
$CONDA_PREFIX/share/sccmec/sccmec-targets.fasta
$CONDA_PREFIX/share/sccmec/sccmec-regions.fasta

The SCCmec command automatically uses these bundled files. Therefore this wrapper does not require a separate Galaxy Data Manager.

Conda requirement

<requirement type="package" version="1.2.0">sccmec</requirement>

Repository layout

sccmec/
├── sccmec.xml
├── .shed.yml
├── README.md
└── test-data/
    └── sccmec_test.fasta

For initial testing, you can use a known working FASTA as:

test-data/sccmec_test.fasta

Testing with Planemo

planemo lint sccmec.xml
planemo test sccmec.xml
planemo serve
planemo shed_lint

Citation

Petit RA III, Read TD. SCCmec typing tool.

DOI: 10.1093/bioinformatics/btac527