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

doi:10.1093/bioinformatics/btv421

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 journal › Article › peer-review

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 language	English
Number of pages	3
Journal	Bioinformatics (Oxford, England)
Volume	Advance Access
Early online date	20 Jul 2015
DOIs	https://doi.org/10.1093/bioinformatics/btv421
Publication status	Published - 2015

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10.1093/bioinformatics/btv421

page2015bioinformatics-advance
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.
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title = "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.",

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

note = "This work was supported by the Wellcome Trust (grant WT 098051). ",

year = "2015",

doi = "10.1093/bioinformatics/btv421",

language = "English",

volume = "Advance Access",

journal = "Bioinformatics (Oxford, England)",

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TY - JOUR

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T2 - rapid large-scale prokaryote pan genome analysis

AU - Page, Andrew J

AU - Cummins, Carla A

AU - Hunt, Martin

AU - Wong, Vanessa K

AU - Reuter, Sandra

AU - Holden, Matthew T G

AU - Fookes, Maria

AU - Falush, Daniel

AU - Keane, Jacqueline A

AU - Parkhill, Julian

N1 - This work was supported by the Wellcome Trust (grant WT 098051).

PY - 2015

Y1 - 2015

N2 - 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.

AB - 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.

U2 - 10.1093/bioinformatics/btv421

DO - 10.1093/bioinformatics/btv421

M3 - Article

C2 - 26198102

SN - 1367-4811

VL - Advance Access

JO - Bioinformatics (Oxford, England)

JF - Bioinformatics (Oxford, England)

ER -

Roary: rapid large-scale prokaryote pan genome analysis

Abstract

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