Roary: rapid large-scale prokaryote pan genome analysis

Andrew J. Page; Carla Cummins; Martin Hunt; Vanessa Wong; Sandra Reuter; Matthew T. G. Holden; María Fookes; Daniel Falush · Bioinformatics · 2015

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Author / responsible party

Andrew J. Page; Carla Cummins; Martin Hunt; Vanessa Wong; Sandra Reuter; Matthew T. G. Holden; María Fookes; Daniel Falush

Publisher

Bioinformatics

Year

2015

Language

English

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UNLABELLED: 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. AVAILABILITY AND IMPLEMENTATION: Roary is implemented in Perl and is freely available under an open source GPLv3 license from http://sanger-pathogens.github.io/Roary CONTACT: roary@sanger.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

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APA 7

Page, A. J, Cummins, C, Hunt, M, Wong, V, Reuter, S, Holden, M. T. G, Fookes, M, & Falush, D. (2015). Roary: rapid large-scale prokaryote pan genome analysis. https://doi.org/10.1093/bioinformatics/btv421

MLA

Page, Andrew J, et al. "Roary: rapid large-scale prokaryote pan genome analysis." 2015. https://doi.org/10.1093/bioinformatics/btv421.

Chicago

Page, Andrew J, Carla Cummins, Martin Hunt, Vanessa Wong, Sandra Reuter, Matthew T. G. Holden, María Fookes, and Daniel Falush. 2015. "Roary: rapid large-scale prokaryote pan genome analysis.". https://doi.org/10.1093/bioinformatics/btv421.

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Page, A. J. et al. 2015, Roary: rapid large-scale prokaryote pan genome analysis, Bioinformatics, available at: https://doi.org/10.1093/bioinformatics/btv421 [Accessed 8 Aug. 2026].

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Title: Roary: rapid large-scale prokaryote pan genome analysis

Author / contributors: Andrew J. Page; Carla Cummins; Martin Hunt; Vanessa Wong; Sandra Reuter; Matthew T. G. Holden; María Fookes; Daniel Falush

Publisher: Bioinformatics

Publication year: 2015

Language: English

Subjects

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Prokaryote; Genome; Perl; Computational biology; Sanger sequencing; Biology; Computer science; Population; DNA sequencing; Gene; Genetics; World Wide Web