Figure 3.

Mycobacterium bovis whole-genome sequencing (WGS) workflow from bacterial isolation to data analysis. SNP: single nucleotide polymorphism. * Time is highly dependable on library kit and sequencing protocol. ** MTBC-specific and general parameters are described in detail in the text, but overall this includes FastQC parameters, minimum established sequencing coverage, contaminating reads, species confirmation, mixed-strain evaluation (depending on the purpose of the analysis), and homogeneous sequencing coverage (after reference genome mapping). MTBC: Mycobacterium tuberculosis complex.