Lighter: fast and memory-efficient sequencing error correction without counting
Identifieur interne : 001045 ( Pmc/Checkpoint ); précédent : 001044; suivant : 001046Lighter: fast and memory-efficient sequencing error correction without counting
Auteurs : Li Song [États-Unis] ; Liliana Florea [États-Unis] ; Ben Langmead [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2014.
Abstract
Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting
The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.
Url:
DOI: 10.1186/s13059-014-0509-9
PubMed: 25398208
PubMed Central: 4248469
Affiliations:
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PMC:4248469Le document en format XML
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xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Johns Hopkins University, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Department of Computer Science, Johns Hopkins University, Baltimore, 21218 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Johns Hopkins University, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Langmead, Ben" sort="Langmead, Ben" uniqKey="Langmead B" first="Ben" last="Langmead">Ben Langmead</name><affiliation wicri:level="3"><nlm:aff id="Aff1">Department of Computer Science, Johns Hopkins University, Baltimore, 21218 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science, Johns Hopkins University, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="3"><nlm:aff id="Aff2">McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205 USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore</wicri:regionArea><placeName><settlement type="city">Baltimore</settlement><region type="state">Maryland</region></placeName></affiliation></author></analytic><series><title level="j">Genome Biology</title><idno type="ISSN">1465-6906</idno><idno type="eISSN">1465-6914</idno><imprint><date when="2014">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting <italic>k</italic>-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input <italic>k</italic>-mers and the other holding <italic>k</italic>-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.</p></sec></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Glenn, Tc" uniqKey="Glenn T">TC Glenn</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct><analytic><author><name sortKey="Pevzner, Pa" uniqKey="Pevzner P">PA Pevzner</name></author><author><name sortKey="Tang, H" uniqKey="Tang H">H Tang</name></author><author><name sortKey="Waterman, Ms" uniqKey="Waterman M">MS Waterman</name></author></analytic></biblStruct><biblStruct><analytic><author><name sortKey="Chaisson, M" uniqKey="Chaisson M">M Chaisson</name></author><author><name sortKey="Pevzner, P" 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<front><journal-meta><journal-id journal-id-type="nlm-ta">Genome Biol</journal-id><journal-title-group><journal-title>Genome Biology</journal-title></journal-title-group><issn pub-type="ppub">1465-6906</issn><issn pub-type="epub">1465-6914</issn><publisher><publisher-name>BioMed Central</publisher-name><publisher-loc>London</publisher-loc></publisher></journal-meta><article-meta><article-id pub-id-type="pmid">25398208</article-id><article-id pub-id-type="pmc">4248469</article-id><article-id pub-id-type="publisher-id">509</article-id><article-id pub-id-type="doi">10.1186/s13059-014-0509-9</article-id><article-categories><subj-group subj-group-type="heading"><subject>Software</subject></subj-group></article-categories><title-group><article-title>Lighter: fast and memory-efficient sequencing error correction without counting</article-title></title-group><contrib-group><contrib contrib-type="author"><name><surname>Song</surname><given-names>Li</given-names></name><address><email>lsong10@jhu.edu</email></address><xref ref-type="aff" rid="Aff1"></xref></contrib><contrib contrib-type="author"><name><surname>Florea</surname><given-names>Liliana</given-names></name><address><email>florea@jhu.edu</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><contrib contrib-type="author" corresp="yes"><name><surname>Langmead</surname><given-names>Ben</given-names></name><address><email>langmea@cs.jhu.edu</email></address><xref ref-type="aff" rid="Aff1"></xref><xref ref-type="aff" rid="Aff2"></xref></contrib><aff id="Aff1"><label></label>Department of Computer Science, Johns Hopkins University, Baltimore, 21218 USA</aff><aff id="Aff2"><label></label>McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, 21205 USA</aff></contrib-group><pub-date pub-type="epub"><day>15</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="pmc-release"><day>15</day><month>11</month><year>2014</year></pub-date><pub-date pub-type="ppub"><year>2014</year></pub-date><volume>15</volume><issue>11</issue><elocation-id>509</elocation-id><history><date date-type="received"><day>27</day><month>5</month><year>2014</year></date><date date-type="accepted"><day>29</day><month>9</month><year>2014</year></date></history><permissions><copyright-statement>© Song et al.; licensee BioMed Central Ltd. 2014</copyright-statement><license license-type="open-access"><license-p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0">http://creativecommons.org/licenses/by/4.0</ext-link>), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication
waiver (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/publicdomain/zero/1.0/">http://creativecommons.org/publicdomain/zero/1.0/</ext-link>) applies to the data made available in this article, unless otherwise
stated.</license-p></license></permissions><abstract id="Abs1"><p>Lighter is a fast, memory-efficient tool for correcting sequencing errors. Lighter avoids counting <italic>k</italic>-mers. Instead, it uses a pair of Bloom filters, one holding a sample of the input <italic>k</italic>-mers and the other holding <italic>k</italic>-mers likely to be correct. As long as the sampling fraction is adjusted in inverse proportion to the depth of sequencing, Bloom filter size can be held constant while maintaining near-constant accuracy. Lighter is parallelized, uses no secondary storage, and is both faster and more memory-efficient than competing approaches while achieving comparable accuracy.</p><sec><title>Electronic supplementary material</title><p>The online version of this article (doi:10.1186/s13059-014-0509-9) contains supplementary material, which is available to authorized users.</p></sec></abstract><custom-meta-group><custom-meta><meta-name>issue-copyright-statement</meta-name><meta-value>© The Author(s) 2014</meta-value></custom-meta></custom-meta-group></article-meta></front></pmc><affiliations><list><country><li>États-Unis</li></country><region><li>Maryland</li></region><settlement><li>Baltimore</li></settlement></list><tree><country name="États-Unis"><region name="Maryland"><name sortKey="Song, Li" sort="Song, Li" uniqKey="Song L" first="Li" last="Song">Li Song</name></region><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name><name sortKey="Florea, Liliana" sort="Florea, Liliana" uniqKey="Florea L" first="Liliana" last="Florea">Liliana Florea</name><name sortKey="Langmead, Ben" sort="Langmead, Ben" uniqKey="Langmead B" first="Ben" last="Langmead">Ben Langmead</name><name sortKey="Langmead, Ben" sort="Langmead, Ben" uniqKey="Langmead B" first="Ben" last="Langmead">Ben Langmead</name></country></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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