Fig. 1

Flow diagram of the SNP cut-off assessment pipeline. Sequences, and their sampling times, are used to infer phylogenetic trees per Mtbc lineage and to estimate mutation rates for these lineages with BEAST. Independently of the phylogenetic tree inference, the sequences are grouped in genetic clusters based on a SNP cut-off. These clusters are used, together with the sampling times of sequences, and the mutation rate of the corresponding Mtbc lineage, to infer transmission trees with phybreak. Finally, inferred transmission events and unconnected cases serve as a reference to assess the performance of SNP cut-offs in determining transmission events.