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Roary: rapid large-scale prokaryote pan genome analysis.

ABSTRACT:

Unlabelled

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.

SUBMITTER: Page AJ

PROVIDER: S-EPMC4817141 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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Roary: rapid large-scale prokaryote pan genome analysis.

Page Andrew J AJ Cummins Carla A CA Hunt Martin M Wong Vanessa K VK Reuter Sandra S Holden Matthew T G MT Fookes Maria M Falush Daniel D Keane Jacqueline A JA Parkhill Julian J

Bioinformatics (Oxford, England) 20150720 22

<h4>Unlabelled</h4>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 resul ...[more]

PMID: 26198102

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