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Bioinformatics. 2015 Nov 15;31(22):3691-3. doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.

Roary: rapid large-scale prokaryote pan genome analysis.

Author information

1
Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge.
2
Pathogen Genomics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, Department of Medicine, University of Cambridge, Cambridge.
3
Department of Medicine, University of Cambridge, Cambridge.
4
School of Medicine, University of St. Andrews, North Haugh, St Andrews and.
5
College of Medicine, Swansea University, Swansea, UK.

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.

AVAILABILITY AND IMPLEMENTATION:

Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary

CONTACT:

roary@sanger.ac.uk

SUPPLEMENTARY INFORMATION:

Supplementary data are available at Bioinformatics online.

PMID:
26198102
PMCID:
PMC4817141
DOI:
10.1093/bioinformatics/btv421
[Indexed for MEDLINE]
Free PMC Article

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