Fast and flexible bacterial genomic epidemiology with PopPUNK

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 ( Pop ulation P artitioning U sing N ucleotide 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…

• BA
  Bill and Melinda Gates Foundation
• WT
  Wellcome Trust

  Award: 098051
• RS
  Royal Society

  Award: 104169/Z/14/Z
• UP
  U.S. Public Health Service

  Awards: AI105168, AI038446
• MR
  Medical Research Council

  Awards: MR/R003076/1, MR/R015600/1
• HE
  H2020 European Research Council

  Award: 742158