Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Identifieur interne : 001895 ( PubMed/Curation ); précédent : 001894; suivant : 001896Trowel: a fast and accurate error correction module for Illumina sequencing reads.
Auteurs : Eun-Cheon Lim [Allemagne] ; Jonas Müller [Allemagne] ; Jörg Hagmann [Allemagne] ; Stefan R. Henz [Allemagne] ; Sang-Tae Kim [Allemagne] ; Detlef Weigel [Allemagne]Source :
- Bioinformatics (Oxford, England) [ 1367-4811 ] ; 2014.
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- methods : High-Throughput Nucleotide Sequencing.
- Algorithms, Software.
Abstract
The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.
DOI: 10.1093/bioinformatics/btu513
PubMed: 25075116
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Henz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Sang Tae" sort="Kim, Sang Tae" uniqKey="Kim S" first="Sang-Tae" last="Kim">Sang-Tae Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Weigel, Detlef" sort="Weigel, Detlef" uniqKey="Weigel D" first="Detlef" last="Weigel">Detlef Weigel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:25075116</idno><idno type="pmid">25075116</idno><idno type="doi">10.1093/bioinformatics/btu513</idno><idno type="wicri:Area/PubMed/Corpus">001895</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001895</idno><idno type="wicri:Area/PubMed/Curation">001895</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001895</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Trowel: a fast and accurate error correction module for Illumina sequencing reads.</title><author><name sortKey="Lim, Eun Cheon" sort="Lim, Eun Cheon" uniqKey="Lim E" first="Eun-Cheon" last="Lim">Eun-Cheon Lim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Muller, Jonas" sort="Muller, Jonas" uniqKey="Muller J" first="Jonas" last="Müller">Jonas Müller</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Hagmann, Jorg" sort="Hagmann, Jorg" uniqKey="Hagmann J" first="Jörg" last="Hagmann">Jörg Hagmann</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Henz, Stefan R" sort="Henz, Stefan R" uniqKey="Henz S" first="Stefan R" last="Henz">Stefan R. Henz</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Kim, Sang Tae" sort="Kim, Sang Tae" uniqKey="Kim S" first="Sang-Tae" last="Kim">Sang-Tae Kim</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author><author><name sortKey="Weigel, Detlef" sort="Weigel, Detlef" uniqKey="Weigel D" first="Detlef" last="Weigel">Detlef Weigel</name><affiliation wicri:level="1"><nlm:affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</nlm:affiliation><country xml:lang="fr">Allemagne</country><wicri:regionArea>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen</wicri:regionArea></affiliation></author></analytic><series><title level="j">Bioinformatics (Oxford, England)</title><idno type="eISSN">1367-4811</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Algorithms</term><term>High-Throughput Nucleotide Sequencing (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Algorithmes</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit ()</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>High-Throughput Nucleotide Sequencing</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Algorithms</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Algorithmes</term><term>Logiciel</term><term>Séquençage nucléotidique à haut débit</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.</div></front></TEI><pubmed><MedlineCitation Status="MEDLINE" IndexingMethod="Curated" Owner="NLM"><PMID Version="1">25075116</PMID><DateCompleted><Year>2015</Year><Month>01</Month><Day>09</Day></DateCompleted><DateRevised><Year>2018</Year><Month>12</Month><Day>02</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1367-4811</ISSN><JournalIssue CitedMedium="Internet"><Volume>30</Volume><Issue>22</Issue><PubDate><Year>2014</Year><Month>Nov</Month><Day>15</Day></PubDate></JournalIssue><Title>Bioinformatics (Oxford, England)</Title><ISOAbbreviation>Bioinformatics</ISOAbbreviation></Journal><ArticleTitle>Trowel: a fast and accurate error correction module for Illumina sequencing reads.</ArticleTitle><Pagination><MedlinePgn>3264-5</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1093/bioinformatics/btu513</ELocationID><Abstract><AbstractText Label="MOTIVATION" NlmCategory="BACKGROUND">The ability to accurately read the order of nucleotides in DNA and RNA is fundamental for modern biology. Errors in next-generation sequencing can lead to many artifacts, from erroneous genome assemblies to mistaken inferences about RNA editing. Uneven coverage in datasets also contributes to false corrections.</AbstractText><AbstractText Label="RESULT" NlmCategory="RESULTS">We introduce Trowel, a massively parallelized and highly efficient error correction module for Illumina read data. Trowel both corrects erroneous base calls and boosts base qualities based on the k-mer spectrum. With high-quality k-mers and relevant base information, Trowel achieves high accuracy for different short read sequencing applications.The latency in the data path has been significantly reduced because of efficient data access and data structures. In performance evaluations, Trowel was highly competitive with other tools regardless of coverage, genome size read length and fragment size.</AbstractText><AbstractText Label="AVAILABILITY AND IMPLEMENTATION" NlmCategory="METHODS">Trowel is written in C++ and is provided under the General Public License v3.0 (GPLv3). It is available at http://trowel-ec.sourceforge.net.</AbstractText><AbstractText Label="CONTACT" NlmCategory="BACKGROUND">euncheon.lim@tue.mpg.de or weigel@tue.mpg.de</AbstractText><AbstractText Label="SUPPLEMENTARY INFORMATION" NlmCategory="BACKGROUND">Supplementary data are available at Bioinformatics online.</AbstractText><CopyrightInformation>© The Author 2014. 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>Lim</LastName><ForeName>Eun-Cheon</ForeName><Initials>EC</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Müller</LastName><ForeName>Jonas</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Hagmann</LastName><ForeName>Jörg</ForeName><Initials>J</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Henz</LastName><ForeName>Stefan R</ForeName><Initials>SR</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Kim</LastName><ForeName>Sang-Tae</ForeName><Initials>ST</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Weigel</LastName><ForeName>Detlef</ForeName><Initials>D</Initials><AffiliationInfo><Affiliation>Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType><PublicationType UI="D013485">Research Support, Non-U.S. Gov't</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2014</Year><Month>07</Month><Day>29</Day></ArticleDate></Article><MedlineJournalInfo><Country>England</Country><MedlineTA>Bioinformatics</MedlineTA><NlmUniqueID>9808944</NlmUniqueID><ISSNLinking>1367-4803</ISSNLinking></MedlineJournalInfo><CitationSubset>IM</CitationSubset><MeshHeadingList><MeshHeading><DescriptorName UI="D000465" MajorTopicYN="N">Algorithms</DescriptorName></MeshHeading><MeshHeading><DescriptorName UI="D059014" MajorTopicYN="N">High-Throughput Nucleotide Sequencing</DescriptorName><QualifierName UI="Q000379" MajorTopicYN="Y">methods</QualifierName></MeshHeading><MeshHeading><DescriptorName UI="D012984" MajorTopicYN="Y">Software</DescriptorName></MeshHeading></MeshHeadingList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="entrez"><Year>2014</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2014</Year><Month>7</Month><Day>31</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2015</Year><Month>1</Month><Day>13</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">25075116</ArticleId><ArticleId IdType="pii">btu513</ArticleId><ArticleId IdType="doi">10.1093/bioinformatics/btu513</ArticleId></ArticleIdList></PubmedData></pubmed></record>Pour manipuler ce document sous Unix (Dilib)
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