Kraken: ultrafast metagenomic sequence classification using exact alignments.
Identifieur interne : 001A39 ( PubMed/Corpus ); précédent : 001A38; suivant : 001A40Kraken: ultrafast metagenomic sequence classification using exact alignments.
Auteurs : Derrick E. Wood ; Steven L. SalzbergSource :
- Genome biology [ 1474-760X ] ; 2014.
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 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/.
DOI: 10.1186/gb-2014-15-3-r46
PubMed: 24580807
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pubmed:24580807Le document en format XML
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<author><name sortKey="Salzberg, Steven L" sort="Salzberg, Steven L" uniqKey="Salzberg S" first="Steven L" last="Salzberg">Steven L. Salzberg</name>
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<series><title level="j">Genome biology</title>
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<profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Archaea (classification)</term>
<term>Archaea (genetics)</term>
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<term>Bacteria (genetics)</term>
<term>Classification</term>
<term>Humans</term>
<term>Metagenome</term>
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<term>Sensitivity and Specificity</term>
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<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>
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