Name: Salmonella-CRISPR-Typing
Owner: C3BI-pasteur-fr
Description: null
Created: 2017-10-26 15:23:37.0
Updated: 2017-10-26 15:25:36.0
Pushed: 2017-12-22 12:38:58.0
Homepage: null
Size: 196
Language: Python
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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:
on3 -m venv crispr_typing
ce crispr_typing/bin/activate
install salmonella_crispr_typing
To check if the installation was successful, try to display the help menu:
pr_typing -h
Salmonella CRISPR Typing tool allows the discovery of spacers and DRs from either a PCR product of a full assembly.
pr_typing your_file.fa
Please, read the help message for advanced features on the tool.
pr_typing --help
In the example folder, you have example files from the following command:
pr_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