Figure 1From: SNIT: SNP identification for strain typingOutline of the SNP identification pipeline. The tandem repeat regions in the input genomes can be masked using the Tandem Repeat Finder (TRF) program. Each input genome is aligned against a user-specified reference genome. The lists of differentiating SNPs and indels between each pair of input genomes are constructed from these pairwise alignments.Back to article page