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Link to original content: http://www.ncbi.nlm.nih.gov/pubmed/26198102
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. 2015 Nov 15;31(22):3691-3.
doi: 10.1093/bioinformatics/btv421. Epub 2015 Jul 20.

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J Page  1 , Carla A Cummins  1 , Martin Hunt  1 , Vanessa K Wong  2 , Sandra Reuter  3 , Matthew T G Holden  4 , Maria Fookes  1 , Daniel Falush  5 , Jacqueline A Keane  1 , Julian Parkhill  1
Affiliations

Roary: rapid large-scale prokaryote pan genome analysis

Andrew J Page et al. Bioinformatics. .

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.

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Figures

Fig. 1.
Fig. 1.
Effect of dataset size on the wall time of multiple applications. Only analysis that completed within 2 days and 60 GB of RAM is shown
See this image and copyright information in PMC

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