Usage

Input files

Genome assemblies in FASTA format. Can be either draft or completed assemblies (completed is better because it reduces the risk of fragmented genes/loci).

Basic usage

staphscan -i *.fasta -o staphscan_output

-i *.fasta : Specifies the input files (assemblies) to be analyzed (.fasta).

-o : Specifies the directory where the output files will be saved.

Modules selection

Module can be run separately, by using the -m parameter:

# select one module

staphscan -i *.fasta -o staphscan_output -m mlst

# select more modules

staphscan -i *.fasta -o staphscan_output -m mlst,spa

To see all modules:

staphscan --list_modules

Check available modules, check version, print help:

staphscan [--list_modules] [--version] [-h]

Output files

Output files are tab-delimited (.tsv) files. Columns included in each output file will depend on the modules that are run.

To use a custom report name:

staphscan --report custom_name

Parameters

Input/Output

-i ASSEMBLIES [ASSEMBLIES ...], --input ASSEMBLIES [ASSEMBLIES ...]
FASTA file(s) for assemblies

-o OUTDIR, --outdir OUTDIR
Directory for storing output files (default: staphscan_results)

--report
Add a custom name for the output report

Modules

--list_modules
Print a list of all available modules and then quit (default: False)

-m MODULES, --modules MODULES:
Comma-delimited list of staphscan modules to use (default: all)

--mlst_update
Download latest database from PubMLST

--db_mlst
Location of the alternative folder containing the mlst database (useful when working in read-only env)

Module-specific parameters are available in the Modules section.

Help

-h, --help
Show a help message and exit

--version
Show program's version number and exit