Modules

StaphSCAN includes a range of modules for typing bacterial genomes. These modules will be run by default, unless specified otherwise by the user (using the -m parameter).

Here a list of the available modules and their functions:

• assembly: Quality control of genome assemblies, including species identification
• mlst: Multi-locus sequence typing (MLST) of Staphylococcus aureus
• spa: spa typing of Staphylococcus aureus
• capsule: Capsular polysaccharide typing of Staphylococcus aureus
• sccmec: SCCmec typing of Staphylococcus aureus
• agr: Accessory gene regulator (agr) typing of Staphylococcus aureus
• resistance: Detection of antimicrobial resistance genes (including clinically relevant mutations)
• virulence: Detection of virulence genes (including clinically relevant mutations)
• biofilm: Detection of biofilm associated genes

For more information on each module, see the respective sections in this documentation.