Kraken Taxonomic Sequence Classification System

Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. 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.

See the Kraken home page for more info.

Let’s assign taxonomic labels to our binning results using Kraken. First, we need to compare the genome bins against the Kraken database:

cd ~/workdir/assembly/megahit_out

qsub -cwd -pe multislot 24 -N kraken -l mtc=1 -b y \
/vol/cmg/bin/kraken --db /vol/metagencourse/krakendb --threads 24 --fasta-input maxbin.001.fasta --output maxbin.001.kraken

If you need the full taxonomic name associated with each input sequence, Kraken provides a script named kraken-translate that produces two different output formats for classified sequences. The script operates on the output of kraken:

kraken-translate --db /vol/metagencourse/krakendb maxbin.001.kraken > maxbin.001.kraken.labels

Does the abundance of the bins match the 16S profile of the community?