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
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_typingTo check if the installation was successful, try to display the help menu:
crispr_typing -hSalmonella CRISPR Typing tool allows the discovery of spacers and DRs from either a PCR product of a full assembly.
crispr_typing your_file.faPlease, read the help message for advanced features on the tool.
crispr_typing --helpIn the example folder, you have example files from the following command:
crispr_typing query.fasta -o seq.output -c -l -e| 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 |
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