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Roary: rapid large-scale prokaryote pan genome analysis

Research output: Contribution to journalArticle

Author(s)

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

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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.
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Original languageEnglish
Number of pages3
JournalBioinformatics (Oxford, England)
VolumeAdvance Access
Early online date20 Jul 2015
DOIs
Publication statusPublished - 2015

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