NB SNP-IT has been re-farctored by Phill Fowler and Michael Hall - this version is now depricated and no longer maintained. Please see https://github.com/philipwfowler/snpit for the most recent version
Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex
SNP-IT allows rapid speciation of fasta files of genomes alligned to NC000962
Usage python SNP-IT.py input_file output_file
Requires: csv, BioPython
The top hit against the reference SNP libraries is printed to stdout. A complete list of absolute and % matches against all subspecies/lineages/sub-lineages is printed to the output_file.
Please email samuel.lipworth@medsci.ox.ac.uk with any queries.