Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.
Identifieur interne : 000640 ( PubMed/Corpus ); précédent : 000639; suivant : 000641Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.
Auteurs : Antoine Limasset ; Jean-François Flot ; Pierre PeterlongoSource :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2020.
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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pubmed:30785192Le 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><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><nlm:affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</nlm:affiliation>
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<author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name>
<affiliation><nlm:affiliation>Inria, CNRS, University of Rennes, IRISA, Rennes, France.</nlm:affiliation>
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<author><name sortKey="Limasset, Antoine" sort="Limasset, Antoine" uniqKey="Limasset A" first="Antoine" last="Limasset">Antoine Limasset</name>
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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><nlm:affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</nlm:affiliation>
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<author><name sortKey="Peterlongo, Pierre" sort="Peterlongo, Pierre" uniqKey="Peterlongo P" first="Pierre" last="Peterlongo">Pierre Peterlongo</name>
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<series><title level="j">Bioinformatics (Oxford, England)</title>
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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>
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<Title>Bioinformatics (Oxford, England)</Title>
<ISOAbbreviation>Bioinformatics</ISOAbbreviation>
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<ArticleTitle>Toward perfect reads: self-correction of short reads via mapping on de Bruijn graphs.</ArticleTitle>
<Pagination><MedlinePgn>1374-1381</MedlinePgn>
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<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>
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<AffiliationInfo><Affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</Affiliation>
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<Author ValidYN="Y"><LastName>Flot</LastName>
<ForeName>Jean-François</ForeName>
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<AffiliationInfo><Affiliation>Evolutionary Biology & Ecology, Université Libre de Bruxelles (ULB), Bruxelles, Belgium.</Affiliation>
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<AffiliationInfo><Affiliation>Interuniversity Institute of Bioinformatics in Brussels - (IB) 2, Brussels, Belgium.</Affiliation>
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<Author ValidYN="Y"><LastName>Peterlongo</LastName>
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<AffiliationInfo><Affiliation>Inria, CNRS, University of Rennes, IRISA, Rennes, France.</Affiliation>
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