MersV1, PubMed, Corpus, bibRecord, 001A39

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Identifieur interne : 001A39 ( PubMed/Corpus ); précédent : 001A38; suivant : 001A40

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Auteurs : Derrick E. Wood ; Steven L. Salzberg

Source :

Genome biology [ 1474-760X ] ; 2014.

RBID : pubmed:24580807

English descriptors

KwdEn :
- Archaea (classification), Archaea (genetics), Bacteria (classification), Bacteria (genetics), Classification, Humans, Metagenome, Metagenomics (methods), Sensitivity and Specificity, Sequence Alignment (methods), Sequence Analysis, DNA (methods), Software.
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

Links to Exploration step

pubmed:24580807

Le 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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<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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Kraken: ultrafast metagenomic sequence classification using exact alignments.

Kraken: ultrafast metagenomic sequence classification using exact alignments.

Source :

English descriptors

Abstract

Links to Exploration step

Le document en format XML

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