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Fast and sensitive taxonomic classification for metagenomics


Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing or metatranscriptomics experiments.

Each sequencing read is assigned to a taxon in the NCBI taxonomy by comparing it to a reference database containing microbial and viral protein sequences. By using protein-level classification, Kaiju achieves a higher sensitivity compared with methods based on nucleotide comparison.

Kaiju can use either the set of available complete genomes from NCBI RefSeq or the microbial subset of the NCBI BLAST non-redundant protein database nr, optionally also including fungi and microbial eukaryotes.

Reads are translated into amino acid sequences, which are then searched in the database using a modified backward search on a memory-efficient implementation of the Burrows-Wheeler transform, which finds maximum exact matches (MEMs), optionally allowing mismatches in the protein alignment.

The search can process up to millions of reads per minute using, for example, only 10 GB RAM with a reference database comprising 4821 complete microbial genomes.

Kaiju can also be used for querying any custom protein database without taxonomic classification, using either protein or nucleotide queries.

Kaiju is described in Menzel, P. et al. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257 (open access).

The program can be downloaded for a local installation or can be accessed via a web server, where reads can be uploaded for online analysis.


The latest version of Kaiju's source code can be downloaded from GitHub either as compressed archive or by cloning the repository via git:

git clone https://github.com/bioinformatics-centre/kaiju.git

Please refer to the README file for installation and usage instructions.

The source code is available under the GNU General Public License 3.

Release notes

Version 1.6.2
Version 1.6.1
Version 1.6.0
Version 1.5.0
Version 1.4.5
Version 1.4.4
Version 1.4.3
Version 1.4.2
Version 1.4.1
Version 1.4
Version 1.3.1
Version 1.3
Version 1.2
Version 1.1
Version 1.0.1
Version 1.0

Previous releases can be downloaded here.


For questions, bug reports or more information about Kaiju, please contact Peter Menzel. Bug reports can also be filed in GitHub's issue tracker.


Menzel P., Ng K.L., Krogh A. (2016) Fast and sensitive taxonomic classification for metagenomics with Kaiju. Nat. Commun. 7:11257

Read the behind the paper post on Nature Microbiology Community.

The program is being developed by Peter Menzel and Anders Krogh at the Bioinformatics Centre, a part of the Section for Computational and RNA Biology at the University of Copenhagen.