StaphSCAN

StaphSCAN is a genome-based tool for Surveillance through Comprehensive Analysis and staNdardized reporting of Staphylococcus aureus.

It integrates the following steps:

• Species identification
• Assembly Qcheck
• MLST typing
• spa typing
• SCCmec typing
• Capsular typing
• Detection of virulence genes (i.e. PVL)
• Detection of biofilm-related genes
• Detection of antimicrobial resistance genes (i.e. mecA)
• Detection of clinically-relevant mutations (i.e. involved in AMR development)

Documentation

A draft documentation is available here

Citation

You can cite StaphSCAN uisng Bollini, R. (2026). StaphSCAN (v0.3.0). Zenodo. https://doi.org/10.5281/zenodo.18458858

Requirements

StaphSCAN has been built to optimize dependecies. It requires:

• python (v3.10 or greater)
• mash
• blast

And the following packages:

• pandas
• biopython
• rauth
• requests

Usage

conda create -n staphscan -c bioconda staphscan -y

conda activate staphscan

staphscan -h

Basic usage

staphscan -i /path/to/genomes/*.fasta -o results_directory

Options

  -h, --help            show this help message and exit
  -i INPUT [INPUT ...], --input INPUT [INPUT ...]
                        Input FASTA files (supports *.fasta)
  -o OUTDIR, --outdir OUTDIR
                        Output directory
  -m MODULES, --modules MODULES
                        Comma-separated list of modules to run (default: "all")
  --list-modules        Generate the list of available modules
  --mlst_update         Update mlst database
  --db_mlst             Custom folder for mlst db                        
  --report REPORT_NAME  Generate a report with a custom name
  --version             Print current version and exit