Fast and flexible bacterial genomic epidemiology with PopPUNK.

ABSTRACT: The routine use of genomics for disease surveillance provides the opportunity for high-resolution bacterial epidemiology. Current whole-genome clustering and multilocus typing approaches do not fully exploit core and accessory genomic variation, and they cannot both automatically identify, and subsequently expand, clusters of significantly similar isolates in large data sets spanning entire species. Here, we describe PopPUNK (Population Partitioning Using Nucleotide K -mers), a software implementing scalable and expandable annotation- and alignment-free methods for population analysis and clustering. Variable-length k-mer comparisons are used to distinguish isolates' divergence in shared sequence and gene content, which we demonstrate to be

SUBMITTER: Lees JA 

PROVIDER: S-EPMC6360808 | biostudies-literature | 2019 Feb

REPOSITORIES: biostudies-literature