[HTML][HTML] Kraken: ultrafast metagenomic sequence classification using exact alignments
DE Wood, SL Salzberg - Genome biology, 2014 - Springer
Genome biology, 2014•Springer
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 …
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 …
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/ .
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