Kraken: ultrafast metagenomic sequence classification using exact alignments
Identifieur interne : 001C04 ( Main/Exploration ); précédent : 001C03; suivant : 001C05Kraken: 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
Affiliations:
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Le document en format XML
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<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>
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<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>
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<keywords scheme="MESH" qualifier="classification" xml:lang="en"><term>Archaea</term>
<term>Bacteria</term>
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<keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Archaea</term>
<term>Bacteria</term>
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<keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Archéobactéries</term>
<term>Bactéries</term>
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<keywords scheme="MESH" qualifier="methods" xml:lang="en"><term>Metagenomics</term>
<term>Sequence Alignment</term>
<term>Sequence Analysis, DNA</term>
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<keywords scheme="MESH" xml:lang="en"><term>Classification</term>
<term>Humans</term>
<term>Metagenome</term>
<term>Sensitivity and Specificity</term>
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<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>
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</div1>
</back>
</TEI>
<affiliations><list><country><li>États-Unis</li>
</country>
<region><li>Maryland</li>
</region>
<settlement><li>College Park (Maryland)</li>
</settlement>
<orgName><li>Université du Maryland</li>
</orgName>
</list>
<tree><country name="États-Unis"><region name="Maryland"><name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name>
</region>
<name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name>
<name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name>
<name sortKey="Wood, Derrick E" sort="Wood, Derrick E" uniqKey="Wood D" first="Derrick E" last="Wood">Derrick E. Wood</name>
</country>
</tree>
</affiliations>
</record>
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