Roary : rapid large-scale prokaryote pan genome analysis
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.
Citation
Page , A J , Cummins , C A , Hunt , M , Wong , V K , Reuter , S , Holden , M T G , Fookes , M , Falush , D , Keane , J A & Parkhill , J 2015 , ' Roary : rapid large-scale prokaryote pan genome analysis ' , Bioinformatics (Oxford, England) , vol. Advance Access . https://doi.org/10.1093/bioinformatics/btv421
Publication
Bioinformatics (Oxford, England)
Status
Peer reviewed
ISSN
1367-4811Type
Journal article
Rights
Copyright The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Description
This work was supported by the Wellcome Trust (grant WT 098051).Collections
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