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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<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>
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<author><name sortKey="Boucher, Christina" sort="Boucher, Christina" uniqKey="Boucher C" first="Christina" last="Boucher">Christina Boucher</name>
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<wicri:cityArea>Department of Computer Science and Engineering, University of California, San Diego, La Jolla</wicri:cityArea>
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<author><name sortKey="Chitsaz, Hamidreza" sort="Chitsaz, Hamidreza" uniqKey="Chitsaz H" first="Hamidreza" last="Chitsaz">Hamidreza Chitsaz</name>
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<series><title level="j">Bioinformatics</title>
<idno type="ISSN">1367-4803</idno>
<idno type="eISSN">1367-4811</idno>
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<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>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<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
. </pmc-comment>
<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>
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