CITATION.bib

@ARTICLE{Lees2019-tw,
  title    = "Fast and flexible bacterial genomic epidemiology with {PopPUNK}",
  author   = "Lees, John A and Harris, Simon R and Tonkin-Hill, Gerry and
              Gladstone, Rebecca A and Lo, Stephanie W and Weiser, Jeffrey N
              and Corander, Jukka and Bentley, Stephen D and Croucher, Nicholas
              J",
  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
              accurate over multiple orders of magnitude using data from both
              simulations and genomic collections representing 10 taxonomically
              widespread species. Connections between closely related isolates
              of the same strain are robustly identified, despite interspecies
              variation in the pairwise distance distributions that reflects
              species' diverse evolutionary patterns. PopPUNK can process
              103-104 genomes in a single batch, with minimal memory use and
              runtimes up to 200-fold faster than existing model-based methods.
              Clusters of strains remain consistent as new batches of genomes
              are added, which is achieved without needing to reanalyze all
              genomes de novo. This facilitates real-time surveillance with
              consistent cluster naming between studies and allows for outbreak
              detection using hundreds of genomes in minutes. Interactive
              visualization and online publication is streamlined through the
              automatic output of results to multiple platforms. PopPUNK has
              been designed as a flexible platform that addresses important
              issues with currently used whole-genome clustering and typing
              methods, and has potential uses across bacterial genetics and
              public health research.",
  journal  = "Genome Res.",
  volume   =  29,
  number   =  2,
  pages    = "304--316",
  month    =  jan,
  year     =  2019,
  language = "en"
}