samlipworth / kvarq-mtbc-snp-barcodes Goto Github PK

Please see the KvarQ documentation, especially the tutorial section for more information

All data is taken from:

"A robust SNP barcode for typing Mycobacterium tuberculosis complex strains" -- Coll et al (2014) doi: 10.1038/ncomms5812

The file coll14.tsv contains the SNPs described in the paper above. The script _summarize.py generates an overview table from scan results, including average coverage of every SNP, and a grid-like listing of which SNPs occured in which genomes as derived, ancestral, and mixed.