2-AIN-506 a 2-AIN-252: Seminár z bioinformatiky (2) a (4)
Leto 2015
Abstrakt

Derrick E. Wood, Steven L. Salzberg. Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome biology, 15(3):R46. 2014.

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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/.