Salmonella CRISPR Typing

CRISPR polymorphism is a powerful tool to subtype Salmonella strains and is now used in routine for epidemiological investigations. This tool gets a CRISPR profile by identifying the presence of known spacers and direct repeats (DRs) in a given sequence based on a catalogue.

This tool is a reimplemntation of a former tool in Perl/CGI developed by G. Guigon

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Installation

Requirements

This tool is developed in Python3 and uses Biopython library.

We recommand the use of a virtual environment to install and run the tool.

To install, run the following commands:

python3 -m venv crispr_typing
source crispr_typing/bin/activate
pip install salmonella_crispr_typing

To check if the installation was successful, try to display the help menu:

crispr_typing -h

How does it work ?

Salmonella CRISPR Typing tool allows the discovery of spacers and DRs from either a PCR product of a full assembly.

crispr_typing your_file.fa

Please, read the help message for advanced features on the tool.

crispr_typing --help

Example

In the example folder, you have example files from the following command:

crispr_typing query.fasta -o seq.output -c -l -e

Output files

Name	content
seq.output	sequence with spacer sequences replaced by their names
seq.bed	BED file of all the spacers found
new_spacers.fa	sequence of new spacers found

References

Fabre L, Zhang J, Guigon G, Le Hello S, Guibert V, Accou-Demartin M, de Romans S, Lim C, Roux C, Passet V, Diancourt L, Guibourdenche M, Issenhuth-Jeanjean S, Achtman M, Brisse S, Sola C, Weill FX. CRISPR typing and subtyping for improved laboratory surveillance of Salmonella infections. PLoS One. 2012;7(5):e36995. DOI:10.1371/journal.pone.0036995