@article {Page019315, author = {Andrew J. Page and Carla A. Cummins and Martin Hunt and Vanessa K. Wong and Sandra Reuter and Matthew T. G. Holden and Maria Fookes and Jacqueline A. Keane and Julian Parkhill}, title = {Roary: Rapid large-scale prokaryote pan genome analysis}, elocation-id = {019315}, year = {2015}, doi = {10.1101/019315}, publisher = {Cold Spring Harbor Laboratory}, abstract = {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.}, URL = {https://www.biorxiv.org/content/early/2015/05/13/019315}, eprint = {https://www.biorxiv.org/content/early/2015/05/13/019315.full.pdf}, journal = {bioRxiv} }