Kraken: ultrafast metagenomic sequence classification using exact alignments
Identifieur interne : 000D04 ( Ncbi/Merge ); précédent : 000D03; suivant : 000D05Kraken: ultrafast metagenomic sequence classification using exact alignments
Auteurs : Derrick E. Wood [États-Unis] ; Steven L. Salzberg [États-Unis]Source :
- Genome Biology [ 1465-6906 ] ; 2014.
Descripteurs français
- KwdFr :
- MESH :
English descriptors
- KwdEn :
- MESH :
- classification : Archaea, Bacteria.
- genetics : Archaea, Bacteria.
- methods : Metagenomics, Sequence Alignment, Sequence Analysis, DNA.
- Classification, Humans, Metagenome, Sensitivity and Specificity, Software.
Abstract
Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of
Url:
DOI: 10.1186/gb-2014-15-3-r46
PubMed: 24580807
PubMed Central: 4053813
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PMC:4053813Le document en format XML
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Wood</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD</wicri:regionArea><placeName><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><keywords scheme="KwdEn" xml:lang="en"><term>Archaea (classification)</term><term>Archaea (genetics)</term><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Classification</term><term>Humans</term><term>Metagenome</term><term>Metagenomics (methods)</term><term>Sensitivity and Specificity</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences ()</term><term>Analyse de séquence d'ADN ()</term><term>Archéobactéries ()</term><term>Archéobactéries (génétique)</term><term>Bactéries ()</term><term>Bactéries (génétique)</term><term>Classification</term><term>Humains</term><term>Logiciel</term><term>Métagénome</term><term>Métagénomique ()</term><term>Sensibilité et spécificité</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Archaea</term><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Archaea</term><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Archéobactéries</term><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Classification</term><term>Humans</term><term>Metagenome</term><term>Sensitivity and Specificity</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Archéobactéries</term><term>Bactéries</term><term>Classification</term><term>Humains</term><term>Logiciel</term><term>Métagénome</term><term>Métagénomique</term><term>Sensibilité et spécificité</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p>Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of <italic>k</italic>-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at <ext-link ext-link-type="uri" xlink:href="http://ccb.jhu.edu/software/kraken/">http://ccb.jhu.edu/software/kraken/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Venter, C" uniqKey="Venter C">C Venter</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K Remington</name></author><author><name sortKey="Heidelberg, J" uniqKey="Heidelberg J">J Heidelberg</name></author><author><name sortKey="Halpern, A" uniqKey="Halpern A">A Halpern</name></author><author><name sortKey="Rusch, D" uniqKey="Rusch D">D Rusch</name></author><author><name sortKey="Eisen, J" uniqKey="Eisen J">J Eisen</name></author><author><name sortKey="Wu, D" uniqKey="Wu D">D Wu</name></author><author><name sortKey="Paulsen, I" uniqKey="Paulsen I">I Paulsen</name></author><author><name sortKey="Nelson, K" uniqKey="Nelson K">K Nelson</name></author><author><name sortKey="Nelson, W" uniqKey="Nelson W">W 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Wood</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PMC</idno><idno type="pmid">24580807</idno><idno type="pmc">4053813</idno><idno type="url">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053813</idno><idno type="RBID">PMC:4053813</idno><idno type="doi">10.1186/gb-2014-15-3-r46</idno><date when="2014">2014</date><idno type="wicri:Area/Pmc/Corpus">000967</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Corpus" wicri:corpus="PMC">000967</idno><idno type="wicri:Area/Pmc/Curation">000967</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Curation">000967</idno><idno type="wicri:Area/Pmc/Checkpoint">001049</idno><idno type="wicri:explorRef" wicri:stream="Pmc" wicri:step="Checkpoint">001049</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en" level="a" type="main">Kraken: ultrafast metagenomic sequence classification using exact alignments</title><author><name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name><affiliation wicri:level="4"><nlm:aff id="I1">Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD</wicri:regionArea><placeName><region type="state">Maryland</region><settlement type="city">College Park (Maryland)</settlement></placeName><orgName type="university">Université du Maryland</orgName></affiliation><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name><affiliation wicri:level="2"><nlm:aff id="I2">Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD</wicri:regionArea><placeName><region type="state">Maryland</region></placeName></affiliation><affiliation wicri:level="2"><nlm:aff id="I3">Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA</nlm:aff><country xml:lang="fr">États-Unis</country><wicri:regionArea>Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD</wicri:regionArea><placeName><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>Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of <italic>k</italic>-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at <ext-link ext-link-type="uri" xlink:href="http://ccb.jhu.edu/software/kraken/">http://ccb.jhu.edu/software/kraken/</ext-link>.</p></div></front><back><div1 type="bibliography"><listBibl><biblStruct><analytic><author><name sortKey="Venter, C" uniqKey="Venter C">C Venter</name></author><author><name sortKey="Remington, K" uniqKey="Remington K">K Remington</name></author><author><name sortKey="Heidelberg, J" uniqKey="Heidelberg J">J Heidelberg</name></author><author><name sortKey="Halpern, A" uniqKey="Halpern A">A Halpern</name></author><author><name sortKey="Rusch, D" uniqKey="Rusch D">D Rusch</name></author><author><name sortKey="Eisen, J" uniqKey="Eisen J">J Eisen</name></author><author><name sortKey="Wu, D" uniqKey="Wu D">D Wu</name></author><author><name sortKey="Paulsen, I" uniqKey="Paulsen I">I Paulsen</name></author><author><name sortKey="Nelson, K" uniqKey="Nelson K">K Nelson</name></author><author><name sortKey="Nelson, W" uniqKey="Nelson W">W 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uniqKey="Ondov B">B Ondov</name></author><author><name sortKey="Bergman, N" uniqKey="Bergman N">N Bergman</name></author><author><name sortKey="Phillippy, A" uniqKey="Phillippy A">A Phillippy</name></author></analytic></biblStruct><biblStruct></biblStruct><biblStruct></biblStruct></listBibl></div1></back></TEI></pmc><pubmed><TEI><teiHeader><fileDesc><titleStmt><title xml:lang="en">Kraken: ultrafast metagenomic sequence classification using exact alignments.</title><author><name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2014">2014</date><idno type="RBID">pubmed:24580807</idno><idno type="pmid">24580807</idno><idno type="doi">10.1186/gb-2014-15-3-r46</idno><idno type="wicri:Area/PubMed/Corpus">001A39</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Corpus" wicri:corpus="PubMed">001A39</idno><idno type="wicri:Area/PubMed/Curation">001A39</idno><idno type="wicri:explorRef" wicri:stream="PubMed" wicri:step="Curation">001A39</idno><idno type="wicri:Area/PubMed/Checkpoint">001857</idno><idno type="wicri:explorRef" wicri:stream="Checkpoint" wicri:step="PubMed">001857</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">Kraken: ultrafast metagenomic sequence classification using exact alignments.</title><author><name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name></author><author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name></author></analytic><series><title level="j">Genome biology</title><idno type="eISSN">1474-760X</idno><imprint><date when="2014" type="published">2014</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Archaea (classification)</term><term>Archaea (genetics)</term><term>Bacteria (classification)</term><term>Bacteria (genetics)</term><term>Classification</term><term>Humans</term><term>Metagenome</term><term>Metagenomics (methods)</term><term>Sensitivity and Specificity</term><term>Sequence Alignment (methods)</term><term>Sequence Analysis, DNA (methods)</term><term>Software</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Alignement de séquences ()</term><term>Analyse de séquence d'ADN ()</term><term>Archéobactéries ()</term><term>Archéobactéries (génétique)</term><term>Bactéries ()</term><term>Bactéries (génétique)</term><term>Classification</term><term>Humains</term><term>Logiciel</term><term>Métagénome</term><term>Métagénomique ()</term><term>Sensibilité et spécificité</term></keywords><keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Archaea</term><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Archaea</term><term>Bacteria</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Archéobactéries</term><term>Bactéries</term></keywords><keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term><term>Sequence Alignment</term><term>Sequence Analysis, DNA</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Classification</term><term>Humans</term><term>Metagenome</term><term>Sensitivity and Specificity</term><term>Software</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Alignement de séquences</term><term>Analyse de séquence d'ADN</term><term>Archéobactéries</term><term>Bactéries</term><term>Classification</term><term>Humains</term><term>Logiciel</term><term>Métagénome</term><term>Métagénomique</term><term>Sensibilité et spécificité</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Kraken is an ultrafast and highly accurate program for assigning taxonomic labels to metagenomic DNA sequences. Previous programs designed for this task have been relatively slow and computationally expensive, forcing researchers to use faster abundance estimation programs, which only classify small subsets of metagenomic data. Using exact alignment of k-mers, Kraken achieves classification accuracy comparable to the fastest BLAST program. In its fastest mode, Kraken classifies 100 base pair reads at a rate of over 4.1 million reads per minute, 909 times faster than Megablast and 11 times faster than the abundance estimation program MetaPhlAn. Kraken is available at http://ccb.jhu.edu/software/kraken/. </div></front></TEI></pubmed></double></record>Pour manipuler ce document sous Unix (Dilib)
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