RT Journal Article
SR Electronic
T1 Roary: Rapid large-scale prokaryote pan genome analysis
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 019315
DO 10.1101/019315
A1 Andrew J. Page
A1 Carla A. Cummins
A1 Martin Hunt
A1 Vanessa K. Wong
A1 Sandra Reuter
A1 Matthew T. G. Holden
A1 Maria Fookes
A1 Jacqueline A. Keane
A1 Julian Parkhill
YR 2015
UL http://biorxiv.org/content/early/2015/05/13/019315.abstract
AB Summary 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 of prokaryotic genomes. We introduce Roary, a tool that rapidly builds large-scale pan genomes, identifying the core and dispensable 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/RoaryContact roary{at}sanger.ac.ukSupplementary information Supplementary data are available at Bioinformatics online.