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- Kraken is a system for assigning taxonomic labels to short DNA
- sequences, usually obtained through metagenomic studies. Previous
- attempts by other bioinformatics software to accomplish this task have
- often used sequence alignment or machine learning techniques that were
- quite slow, leading to the development of less sensitive but much faster
- abundance estimation programs. Kraken aims to achieve high sensitivity
- and high speed by utilizing exact alignments of k-mers and a novel
- classification algorithm.
- In its fastest mode of operation, for a simulated metagenome of 100 bp
- reads, Kraken processed over 4 million reads per minute on a single
- core, over 900 times faster than Megablast and over 11 times faster than
- the abundance estimation program MetaPhlAn. Kraken's accuracy is
- comparable with Megablast, with slightly lower sensitivity and very high
- precision.
- REFERENCE
- Wood DE, Salzberg SL
- Kraken: ultrafast metagenomic sequence classification using exact
- alignments.
- Genome Biology 2014, 15:R46.
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