SEQuel: improving the accuracy of genome assemblies
Identifieur interne : 000B07 ( Pmc/Curation ); précédent : 000B06; suivant : 000B08SEQuel: improving the accuracy of genome assemblies
Auteurs : Roy Ronen ; Christina Boucher [États-Unis] ; Hamidreza Chitsaz [États-Unis] ; Pavel Pevzner [États-Unis]Source :
- Bioinformatics [ 1367-4803 ] ; 2012.
Abstract
Url:
DOI: 10.1093/bioinformatics/bts219
PubMed: 22689760
PubMed Central: 3371851
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<record><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">SEQuel: improving the accuracy of genome assemblies</title><author><name sortKey="Ronen, Roy" sort="Ronen, Roy" uniqKey="Ronen R" first="Roy" last="Ronen">Roy Ronen</name><affiliation><nlm:aff id="AFF1">Bioinformatics Graduate Program,</nlm:aff></affiliation></author><author><name sortKey="Boucher, Christina" sort="Boucher, Christina" uniqKey="Boucher C" first="Christina" last="Boucher">Christina Boucher</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Computer Science and Engineering, University of California, San Diego, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Chitsaz, Hamidreza" sort="Chitsaz, Hamidreza" uniqKey="Chitsaz H" first="Hamidreza" last="Chitsaz">Hamidreza Chitsaz</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Computer Science, Wayne State University, Detroit, MI 48202, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Wayne State University, Detroit, MI 48202</wicri:regionArea></affiliation></author><author><name sortKey="Pevzner, Pavel" sort="Pevzner, Pavel" uniqKey="Pevzner P" first="Pavel" last="Pevzner">Pavel Pevzner</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Computer Science and Engineering, University of California, San Diego, La Jolla</wicri:cityArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">22689760</idno><idno type="pmc">3371851</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371851</idno><idno type="RBID">PMC:3371851</idno><idno type="doi">10.1093/bioinformatics/bts219</idno><date when="2012">2012</date><idno type="wicri:Area/Pmc/Corpus">000B07</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000B07</idno><idno type="wicri:Area/Pmc/Curation">000B07</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000B07</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">SEQuel: improving the accuracy of genome assemblies</title><author><name sortKey="Ronen, Roy" sort="Ronen, Roy" uniqKey="Ronen R" first="Roy" last="Ronen">Roy Ronen</name><affiliation><nlm:aff id="AFF1">Bioinformatics Graduate Program,</nlm:aff></affiliation></author><author><name sortKey="Boucher, Christina" sort="Boucher, Christina" uniqKey="Boucher C" first="Christina" last="Boucher">Christina Boucher</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Computer Science and Engineering, University of California, San Diego, La Jolla</wicri:cityArea></affiliation></author><author><name sortKey="Chitsaz, Hamidreza" sort="Chitsaz, Hamidreza" uniqKey="Chitsaz H" first="Hamidreza" last="Chitsaz">Hamidreza Chitsaz</name><affiliation wicri:level="1"><nlm:aff id="AFF1">Department of Computer Science, Wayne State University, Detroit, MI 48202, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Wayne State University, Detroit, MI 48202</wicri:regionArea></affiliation></author><author><name sortKey="Pevzner, Pavel" sort="Pevzner, Pavel" uniqKey="Pevzner P" first="Pavel" last="Pevzner">Pavel Pevzner</name><affiliation wicri:level="2"><nlm:aff wicri:cut=" and" id="AFF1">Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093</nlm:aff><country xml:lang="fr">États-Unis</country><placeName><region type="state">Californie</region></placeName><wicri:cityArea>Department of Computer Science and Engineering, University of California, San Diego, La Jolla</wicri:cityArea></affiliation></author></analytic><series><title level="j">Bioinformatics</title><idno type="ISSN">1367-4803</idno><idno type="eISSN">1367-4811</idno><imprint><date when="2012">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><bold>Motivation:</bold> Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop <italic>SEQuel</italic>, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the <italic>positional de Bruijn graph</italic>, a graph structure that models <italic>k</italic>-mers within reads while incorporating the approximate positions of reads into the model.</p><p><bold>Results:</bold> SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell <italic>Escherichia coli</italic> data by almost half, and corrected between 30% and 94% of the substitution errors. Further, we show SEQuel is imperative to improving single-cell assembly, which is inherently more challenging due to higher error rates and non-uniform coverage; over half of the small indels, and substitution errors in the single-cell assemblies were corrected. We apply SEQuel to the recently assembled Deltaproteobacterium <italic>SAR324</italic> genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions, deletions and substitutions) to refine this assembly.</p><p><bold>Availability:</bold> SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at <ext-link ext-link-type="uri" xlink:href="http://bix.ucsd.edu/SEQuel/">http://bix.ucsd.edu/SEQuel/</ext-link>.</p><p><bold>Contact:</bold><email>ppevzner@cs.ucsd.edu</email></p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Alkan, S" uniqKey="Alkan S">S. Alkan</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bankevich, A" uniqKey="Bankevich A">A. Bankevich</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Bentley, D R" uniqKey="Bentley D">D.R. 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Green</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Ewing, B" uniqKey="Ewing B">B. Ewing</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Mckenna, A" uniqKey="Mckenna A">A. McKenna</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hannenhalli, S" uniqKey="Hannenhalli S">S. Hannenhalli</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Hirschberg, D S" uniqKey="Hirschberg D">D.S. Hirschberg</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Huang, S" uniqKey="Huang S">S. Huang</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Idury, R M" uniqKey="Idury R">R.M. Idury</name></author><author><name sortKey="Waterman, M S" uniqKey="Waterman M">M.S. Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Kececioglu, J" uniqKey="Kececioglu J">J. 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Bioinformatics</journal-id><journal-id journal-id-type="iso-abbrev">Bioinformatics</journal-id><journal-id journal-id-type="publisher-id">bioinformatics</journal-id><journal-id journal-id-type="hwp">bioinfo</journal-id><journal-title-group><journal-title>Bioinformatics</journal-title></journal-title-group><issn pub-type="ppub">1367-4803</issn><issn pub-type="epub">1367-4811</issn><publisher><publisher-name>Oxford University Press</publisher-name></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">22689760</article-id><article-id pub-id-type="pmc">3371851</article-id><article-id pub-id-type="doi">10.1093/bioinformatics/bts219</article-id><article-id pub-id-type="publisher-id">bts219</article-id><article-categories><subj-group subj-group-type="heading"><subject>Ismb 2012 Proceedings Papers Committee July 15 to July 19, 2012, Long Beach, Ca, Usa</subject></subj-group><subj-group><subject>Original Papers</subject><subj-group><subject>Sequence Analysis</subject></subj-group></subj-group></article-categories><title-group><article-title>SEQuel: improving the accuracy of genome assemblies</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Ronen</surname><given-names>Roy</given-names></name><xref ref-type="aff" rid="AFF1"><sup>1</sup></xref><xref ref-type="author-notes" rid="FN1"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Boucher</surname><given-names>Christina</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="author-notes" rid="FN1"><sup>†</sup></xref></contrib><contrib contrib-type="author"><name><surname>Chitsaz</surname><given-names>Hamidreza</given-names></name><xref ref-type="aff" rid="AFF1"><sup>3</sup></xref></contrib><contrib contrib-type="author"><name><surname>Pevzner</surname><given-names>Pavel</given-names></name><xref ref-type="aff" rid="AFF1"><sup>2</sup></xref><xref ref-type="corresp" rid="COR1"><sup>*</sup></xref></contrib></contrib-group><aff id="AFF1"><sup>1</sup>Bioinformatics Graduate Program,<sup>2</sup>Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA 92093 and<sup>3</sup>Department of Computer Science, Wayne State University, Detroit, MI 48202, USA</aff><author-notes><corresp id="COR1">* To whom correspondence should be addressed.</corresp><fn id="FN1"><p><sup>†</sup>The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.</p></fn></author-notes><pub-date pub-type="ppub"><day>15</day><month>6</month><year>2012</year></pub-date><pub-date pub-type="epub"><day>9</day><month>6</month><year>2012</year></pub-date><pub-date pub-type="pmc-release"><day>9</day><month>6</month><year>2012</year></pub-date><pmc-comment> PMC Release delay is 0 months and 0 days and was based on the
<volume>28</volume><issue>12</issue><fpage>i188</fpage><lpage>i196</lpage><permissions><copyright-statement>© The Author(s) 2012. Published by Oxford University Press.</copyright-statement><copyright-year>2012</copyright-year><license license-type="creative-commons" xlink:href="http://creativecommons.org/licenses/by-nc/3.0"><license-p><pmc-comment>CREATIVE COMMONS</pmc-comment>This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by-nc/3.0">http://creativecommons.org/licenses/by-nc/3.0</ext-link>), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.</license-p></license></permissions><abstract><p><bold>Motivation:</bold> Assemblies of next-generation sequencing (NGS) data, although accurate, still contain a substantial number of errors that need to be corrected after the assembly process. We develop <italic>SEQuel</italic>, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the <italic>positional de Bruijn graph</italic>, a graph structure that models <italic>k</italic>-mers within reads while incorporating the approximate positions of reads into the model.</p><p><bold>Results:</bold> SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell <italic>Escherichia coli</italic> data by almost half, and corrected between 30% and 94% of the substitution errors. Further, we show SEQuel is imperative to improving single-cell assembly, which is inherently more challenging due to higher error rates and non-uniform coverage; over half of the small indels, and substitution errors in the single-cell assemblies were corrected. We apply SEQuel to the recently assembled Deltaproteobacterium <italic>SAR324</italic> genome, which is the first bacterial genome with a comprehensive single-cell genome assembly, and make over 800 changes (insertions, deletions and substitutions) to refine this assembly.</p><p><bold>Availability:</bold> SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at <ext-link ext-link-type="uri" xlink:href="http://bix.ucsd.edu/SEQuel/">http://bix.ucsd.edu/SEQuel/</ext-link>.</p><p><bold>Contact:</bold><email>ppevzner@cs.ucsd.edu</email></p></abstract><counts><page-count count="9"></page-count></counts></article-meta></front></pmc></record>Pour manipuler ce document sous Unix (Dilib)
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