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Roary : rapid large-scale prokaryote pan genome analysis

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dc.contributor.authorPage, Andrew J
dc.contributor.authorCummins, Carla A
dc.contributor.authorHunt, Martin
dc.contributor.authorWong, Vanessa K
dc.contributor.authorReuter, Sandra
dc.contributor.authorHolden, Matthew T G
dc.contributor.authorFookes, Maria
dc.contributor.authorFalush, Daniel
dc.contributor.authorKeane, Jacqueline A
dc.contributor.authorParkhill, Julian
dc.date.accessioned2015-09-29T14:40:01Z
dc.date.available2015-09-29T14:40:01Z
dc.date.issued2015
dc.identifier.citationPage , 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/btv421en
dc.identifier.issn1367-4811
dc.identifier.otherPURE: 204592001
dc.identifier.otherPURE UUID: 0d246e9f-ea0c-440c-9c73-a3ee91b45b01
dc.identifier.otherPubMed: 26198102
dc.identifier.otherScopus: 84947793096
dc.identifier.otherORCID: /0000-0002-4958-2166/work/60196465
dc.identifier.otherWOS: 000365134700022
dc.identifier.urihttps://hdl.handle.net/10023/7563
dc.descriptionThis work was supported by the Wellcome Trust (grant WT 098051).en
dc.description.abstractA 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.
dc.format.extent3
dc.language.isoeng
dc.relation.ispartofBioinformatics (Oxford, England)en
dc.rightsCopyright 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.en
dc.subjectR Medicineen
dc.subjectQH301 Biologyen
dc.subjectQA75 Electronic computers. Computer scienceen
dc.subjectNDASen
dc.subject.lccRen
dc.subject.lccQH301en
dc.subject.lccQA75en
dc.titleRoary : rapid large-scale prokaryote pan genome analysisen
dc.typeJournal articleen
dc.description.versionPublisher PDFen
dc.contributor.institutionUniversity of St Andrews. School of Medicineen
dc.contributor.institutionUniversity of St Andrews. Infection Groupen
dc.contributor.institutionUniversity of St Andrews. Biomedical Sciences Research Complexen
dc.identifier.doihttps://doi.org/10.1093/bioinformatics/btv421
dc.description.statusPeer revieweden


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