Spoligotype Mycobacterium Tuberculosis

Spoligotyping (Spacer Oligonucleotide Typing) is a method for typing Mycobacterium tuberculosis based on the presence/absence of 43 spacer oligonucleotides. Originally, this was a PCR-based assay done in the lab. The traditional method has been adapted for next-generation sequencing (NGS) data, enabling in silico spoligotyping directly from whole-genome sequencing data.

Spoligotype Mycobacterium Tuberculosis offers spoligotyping of M. tuberculosis isolates from NGS reads. The tool works by searching for the 43 spacer sequences [Van Embden et al., 2000] in reads obtained from M. tuberculosis samples and counting the number of times a match is found. Presence/absence is determined as a binary code, which is then translated into octal code, lineage, and SIT (Shared International Type) using SpolLineages [Couvin et al., 2020].