MersV1, PubMed, Checkpoint, bibRecord, 000039

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Identifieur interne : 000039 ( PubMed/Checkpoint ); précédent : 000038; suivant : 000040

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Auteurs : Antoine Limasset [Belgique] ; Jean-François Flot [Belgique] ; Pierre Peterlongo [France]

Source :

Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.

RBID : pubmed:30785192

Abstract

Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information.

DOI: 10.1093/bioinformatics/btz102
PubMed: 30785192

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Le document en format XML

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<author><name sortKey="Limasset, Antoine" sort="Limasset, Antoine" uniqKey="Limasset A" first="Antoine" last="Limasset">Antoine Limasset</name>
<affiliation wicri:level="4"><nlm:affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</nlm:affiliation>
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<orgName type="university">Université libre de Bruxelles</orgName>
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<author><name sortKey="Flot, Jean Francois" sort="Flot, Jean Francois" uniqKey="Flot J" first="Jean-François" last="Flot">Jean-François Flot</name>
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<author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name>
<affiliation wicri:level="3"><nlm:affiliation>Inria, CNRS, University of Rennes, IRISA, Rennes, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
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<sourceDesc><biblStruct><analytic><title xml:lang="en">Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.</title>
<author><name sortKey="Limasset, Antoine" sort="Limasset, Antoine" uniqKey="Limasset A" first="Antoine" last="Limasset">Antoine Limasset</name>
<affiliation wicri:level="4"><nlm:affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</nlm:affiliation>
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<author><name sortKey="Flot, Jean Francois" sort="Flot, Jean Francois" uniqKey="Flot J" first="Jean-François" last="Flot">Jean-François Flot</name>
<affiliation wicri:level="4"><nlm:affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</nlm:affiliation>
<country xml:lang="fr">Belgique</country>
<wicri:regionArea>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles</wicri:regionArea>
<placeName><settlement type="city">Bruxelles</settlement>
<region nuts="2">Région de Bruxelles-Capitale</region>
</placeName>
<orgName type="university">Université libre de Bruxelles</orgName>
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<author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name>
<affiliation wicri:level="3"><nlm:affiliation>Inria, CNRS, University of Rennes, IRISA, Rennes, France.</nlm:affiliation>
<country xml:lang="fr">France</country>
<wicri:regionArea>Inria, CNRS, University of Rennes, IRISA, Rennes</wicri:regionArea>
<placeName><region type="region">Région Bretagne</region>
<region type="old region">Région Bretagne</region>
<settlement type="city">Rennes</settlement>
</placeName>
</affiliation>
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</analytic>
<series><title level="j">Bioinformatics (Oxford, England)</title>
<idno type="eISSN">1367-4811</idno>
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<front><div type="abstract" xml:lang="en">Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information.</div>
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<pubmed><MedlineCitation Status="In-Data-Review" Owner="NLM"><PMID Version="1">30785192</PMID>
<DateRevised><Year>2020</Year>
<Month>03</Month>
<Day>06</Day>
</DateRevised>
<Article PubModel="Print"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN>
<JournalIssue CitedMedium="Internet"><Volume>36</Volume>
<Issue>5</Issue>
<PubDate><Year>2020</Year>
<Month>Mar</Month>
<Day>01</Day>
</PubDate>
</JournalIssue>
<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
</Journal>
<ArticleTitle>Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.</ArticleTitle>
<Pagination><MedlinePgn>1374-1381</MedlinePgn>
</Pagination>
<ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btz102</ELocationID>
<Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">Short-read accuracy is important for downstream analyses such as genome assembly and hybrid long-read correction. Despite much work on short-read correction, present-day correctors either do not scale well on large datasets or consider reads as mere suites of k-mers, without taking into account their full-length sequence information.</AbstractText>
<AbstractText Label="RESULTS" NlmCategory="RESULTS">We propose a new method to correct short reads using de Bruijn graphs and implement it as a tool called Bcool. As a first step, Bcool constructs a compacted de Bruijn graph from the reads. This graph is filtered on the basis of k-mer abundance then of unitig abundance, thereby removing most sequencing errors. The cleaned graph is then used as a reference on which the reads are mapped to correct them. We show that this approach yields more accurate reads than k-mer-spectrum correctors while being scalable to human-size genomic datasets and beyond.</AbstractText>
<AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">The implementation is open source, available at http://github.com/Malfoy/BCOOL under the Affero GPL license and as a Bioconda package.</AbstractText>
<AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText>
<CopyrightInformation>© The Author(s) 2019. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.</CopyrightInformation>
</Abstract>
<AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Limasset</LastName>
<ForeName>Antoine</ForeName>
<Initials>A</Initials>
<AffiliationInfo><Affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Flot</LastName>
<ForeName>Jean-François</ForeName>
<Initials>JF</Initials>
<AffiliationInfo><Affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</Affiliation>
</AffiliationInfo>
<AffiliationInfo><Affiliation>Interuniversity Institute of Bioinformatics in Brussels - (IB) 2, Brussels, Belgium.</Affiliation>
</AffiliationInfo>
</Author>
<Author ValidYN="Y"><LastName>Peterlongo</LastName>
<ForeName>Pierre</ForeName>
<Initials>P</Initials>
<AffiliationInfo><Affiliation>Inria, CNRS, University of Rennes, IRISA, Rennes, France.</Affiliation>
</AffiliationInfo>
</Author>
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<Language>eng</Language>
<PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType>
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<MedlineJournalInfo><Country>England</Country>
<MedlineTA>Bioinformatics</MedlineTA>
<NlmUniqueID>9808944</NlmUniqueID>
<ISSNLinking>1367-4803</ISSNLinking>
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<CitationSubset>IM</CitationSubset>
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<PubmedData><History><PubMedPubDate PubStatus="received"><Year>2018</Year>
<Month>07</Month>
<Day>23</Day>
</PubMedPubDate>
<PubMedPubDate PubStatus="revised"><Year>2019</Year>
<Month>01</Month>
<Day>07</Day>
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<PubMedPubDate PubStatus="accepted"><Year>2019</Year>
<Month>02</Month>
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<affiliations><list><country><li>Belgique</li>
<li>France</li>
</country>
<region><li>Région Bretagne</li>
<li>Région de Bruxelles-Capitale</li>
</region>
<settlement><li>Bruxelles</li>
<li>Rennes</li>
</settlement>
<orgName><li>Université libre de Bruxelles</li>
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<tree><country name="Belgique"><region name="Région de Bruxelles-Capitale"><name sortKey="Limasset, Antoine" sort="Limasset, Antoine" uniqKey="Limasset A" first="Antoine" last="Limasset">Antoine Limasset</name>
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<name sortKey="Flot, Jean Francois" sort="Flot, Jean Francois" uniqKey="Flot J" first="Jean-François" last="Flot">Jean-François Flot</name>
</country>
<country name="France"><region name="Région Bretagne"><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name>
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</record>

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Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.

Source :

Abstract

Links toward previous steps (curation, corpus...)

Links to Exploration step

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri

Pour générer des pages wiki