SNP-IT: Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex.
Whole genome SNP based identification of members of the Mycobacterium tuberculosis complex. Based on code originally written by Samuel Lipworth and turned into a package by Philip Fowler.
SNP-IT allows rapid Mycobacterial speciation of VCF or FASTA files aligned to NC000962 (H37rV).
With an activated Bioconda channel (see 2. Set up channels), install with:
conda install mtb-snp-it
and update with:
conda update mtb-snp-it
or use the docker container:
docker pull quay.io/biocontainers/mtb-snp-it:<tag>
(see mtb-snp-it/tags for valid values for