CCB » Software » Kraken

About Kraken

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.

Kraken is written in C++ and Perl, and is designed for use with the Linux operating system.


Accuracy and speed

Although we tested Kraken on real sequence data from isolate genomes, the biggest challenge for an exact alignment approach is that of maintaining sensitivity in the face of high divergence from the training data (in this case, Kraken's genomic library). To address the concern of Kraken's sensitivity with such sequences, we created a simulated metagenomic dataset containing simulated 100 bp reads with high sequencing error (2.1% SNP rate, 1.1% indel rate). Below are the results of using various classifiers on this dataset, with accuracy evaluated on a per-read basis:

Classifier Genus
Naïve Bayes Classifier 97.64 97.64 7
PhymmBL 96.11 96.11 76
PhymmBL (conf. > 0.65) 99.08 95.45 76
Megablast w/ best hit 96.93 93.67 4511
Kraken 99.90 91.25 1307161
Kraken (quick operation) 99.92 89.54 4101162
MiniKraken (Kraken w/ 4GB DB) 99.95 65.87 1441476
MiniKraken (quick operation) 99.98 65.31 2693119
MetaPhlAn n/a n/a 370770


Wood DE, Salzberg SL: Kraken: ultrafast metagenomic sequence classification using exact alignments. Genome Biology 2014, 15:R46.


We encourage users to share their questions and experiences with Kraken. We have established a users group (Kraken-users on Google Groups) for discussion, as well as an email address for direct questions (


Derrick Wood