SNP Comparison and phylogenetic analysis for TB

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The purpose of this training video is to provide state and local tuberculosis (TB) control program staff with information from CDC’s Division of TB Elimination (DTBE) on the methods for performing whole-genome single nucleotide polymorphism (SNP) comparison and building phylogenetic trees. Details of each of the steps involved are presented, including reference-based assembly, identification of SNPs relative to the reference, filtering of SNPS, mapping the high-quality SNPs on to a phylogenetic tree, and determining placement of the most recent common ancestor. Considerations for how adding or removing isolates from the comparison affects results and a case study involving a patient with a mixed TB infection are presented.

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