SEQuel: improving the accuracy of genome assemblies.
Identifieur interne : 001D75 ( PubMed/Corpus ); précédent : 001D74; suivant : 001D76SEQuel: improving the accuracy of genome assemblies.
Auteurs : Roy Ronen ; Christina Boucher ; Hamidreza Chitsaz ; Pavel PevznerSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2012.
English descriptors
- KwdEn :
- MESH :
- genetics : Escherichia coli.
- methods : Computational Biology, Sequence Analysis, DNA.
- Algorithms, Contig Mapping, Genome, Bacterial, INDEL Mutation.
Abstract
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 SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.
DOI: 10.1093/bioinformatics/bts219
PubMed: 22689760
Links to Exploration step
pubmed:22689760Le document en format XML
<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:affiliation>Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Boucher, Christina" sort="Boucher, Christina" uniqKey="Boucher C" first="Christina" last="Boucher">Christina Boucher</name></author><author><name sortKey="Chitsaz, Hamidreza" sort="Chitsaz, Hamidreza" uniqKey="Chitsaz H" first="Hamidreza" last="Chitsaz">Hamidreza Chitsaz</name></author><author><name sortKey="Pevzner, Pavel" sort="Pevzner, Pavel" uniqKey="Pevzner P" first="Pavel" last="Pevzner">Pavel Pevzner</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2012">2012</date><idno type="RBID">pubmed:22689760</idno><idno type="pmid">22689760</idno><idno type="doi">10.1093/bioinformatics/bts219</idno><idno type="wicri:Area/PubMed/Corpus">001D75</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001D75</idno></publicationStmt><sourceDesc><biblStruct><analytic><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:affiliation>Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.</nlm:affiliation></affiliation></author><author><name sortKey="Boucher, Christina" sort="Boucher, Christina" uniqKey="Boucher C" first="Christina" last="Boucher">Christina Boucher</name></author><author><name sortKey="Chitsaz, Hamidreza" sort="Chitsaz, Hamidreza" uniqKey="Chitsaz H" first="Hamidreza" last="Chitsaz">Hamidreza Chitsaz</name></author><author><name sortKey="Pevzner, Pavel" sort="Pevzner, Pavel" uniqKey="Pevzner P" first="Pavel" last="Pevzner">Pavel Pevzner</name></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2012" type="published">2012</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>Computational Biology (methods)</term><term>Contig Mapping</term><term>Escherichia coli (genetics)</term><term>Genome, Bacterial</term><term>INDEL Mutation</term><term>Sequence Analysis, DNA (methods)</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Escherichia coli</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Computational Biology</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Contig Mapping</term><term>Genome, Bacterial</term><term>INDEL Mutation</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">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 SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">22689760</PMID><DateCompleted><Year>2013</Year><Month>01</Month><Day>31</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>01</Day></DateRevised><Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>28</Volume><Issue>12</Issue><PubDate><Year>2012</Year><Month>Jun</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>SEQuel: improving the accuracy of genome assemblies.</ArticleTitle><Pagination><MedlinePgn>i188-96</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/bts219</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">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 SEQuel, a tool that corrects errors (i.e. insertions, deletions and substitution errors) in the assembled contigs. Fundamental to the algorithm behind SEQuel is the positional de Bruijn graph, a graph structure that models k-mers within reads while incorporating the approximate positions of reads into the model.</AbstractText><AbstractText Label="RESULTS" NlmCategory="RESULTS">SEQuel reduced the number of small insertions and deletions in the assemblies of standard multi-cell Escherichia coli 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 SAR324 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.</AbstractText><AbstractText Label="AVAILABILITY" NlmCategory="BACKGROUND">SEQuel can be used as a post-processing step in combination with any NGS assembler and is freely available at http://bix.ucsd.edu/SEQuel/.</AbstractText></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Ronen</LastName><ForeName>Roy</ForeName><Initials>R</Initials><AffiliationInfo><Affiliation>Bioinformatics Graduate Program, University of California, San Diego, La Jolla, CA 92093, USA.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Boucher</LastName><ForeName>Christina</ForeName><Initials>C</Initials></Author><Author ValidYN="Y"><LastName>Chitsaz</LastName><ForeName>Hamidreza</ForeName><Initials>H</Initials></Author><Author ValidYN="Y"><LastName>Pevzner</LastName><ForeName>Pavel</ForeName><Initials>P</Initials></Author></AuthorList><Language>eng</Language><GrantList CompleteYN="Y"><Grant><GrantID>P41 RR024851</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant><Grant><GrantID>3P41RR024851-02S1</GrantID><Acronym>RR</Acronym><Agency>NCRR NIH HHS</Agency><Country>United States</Country></Grant></GrantList><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D052061">Research Support, N.I.H., Extramural</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType><PublicationType UI="D013486">Research Support, U.S. Gov't, 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