Roary: rapid large-scale prokaryote pan genome analysis

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

Research output: Contribution to journalArticlepeer-review

3058 Citations (Scopus)
1 Downloads (Pure)

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

Fingerprint

Dive into the research topics of 'Roary: rapid large-scale prokaryote pan genome analysis'. Together they form a unique fingerprint.

Cite this