title: Roary: rapid large-scale prokaryote pan genome analysis.
abstract: A typical prokaryote population sequencing study can now consist of hundreds or thousands of isolates. Interrogating these datasets can provide detailed insights into the genetic structure of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and accessory genes. Roary makes construction of the pan genome of thousands of prokaryote samples possible on a standard desktop without compromising on the accuracy of results. Using a single CPU Roary can produce a pan genome consisting of 1000 isolates in 4.5 hours using 13 GB of RAM, with further speedups possible using multiple processors.
  
  
  METHODS
  Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary
  
  
  BACKGROUND
  roary@sanger.ac.uk
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Page
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Carla A
authors.initials: CA
authors.lastname: Cummins
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Martin
authors.initials: M
authors.lastname: Hunt
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Department of Medicine, University of Cambridge, Cambridge.
authors.forename: Vanessa K
authors.initials: VK
authors.lastname: Wong
authors.affiliation: Department of Medicine, University of Cambridge, Cambridge.
authors.forename: Sandra
authors.initials: S
authors.lastname: Reuter
authors.affiliation: School of Medicine, University of St. Andrews, North Haugh, St Andrews and.
authors.forename: Matthew T G
authors.initials: MT
authors.lastname: Holden
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Maria
authors.initials: M
authors.lastname: Fookes
authors.affiliation: College of Medicine, Swansea University, Swansea, UK.
authors.forename: Daniel
authors.initials: D
authors.lastname: Falush
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Jacqueline A
authors.initials: JA
authors.lastname: Keane
authors.affiliation: Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
authors.forename: Julian
authors.initials: J
authors.lastname: Parkhill
mesh_terms: D003198:Computer Simulation; D030541:Databases, Genetic; D016680:Genome, Bacterial; D011387:Prokaryotic Cells / Q000378:metabolism*; D012485:Salmonella typhi / Q000235:genetics; D012984:Software