Kraken 2 Code Download

MiniKraken2 Downloads (UPDATE: 2019/04/23)

Users with low-memory computing environments may be unable to load a full Kraken standard library (~30GB as of 09/2018) into RAM. Therefore, we provide here two MiniKraken2 databases that require only 8GB of RAM for classification. The databases were built by using the --max-db-size option, which downsamples the minimizers in the standard Kraken 2 database using a hash function.


Bracken files are included in the above MiniKraken2 database downloads for 100mers, 150mers, and 200mers. To perform a Bracken analysis for other read lengths, contact Jennifer lu.

The challenge with downsampling to create the minimized databases is maintaining sensitivity. To address this concern, we measured accuracy with two datasets (HiSeq and MiSeq) from the original Kraken publication that consist of single-ended microbial isolate reads mixed in equal proportions. Below are the results for Kraken 1 and Kraken 2 using the original standard databases and the 8GB MiniKraken databases: MiniKraken1v2_Accuracy

Additional Pre-built Databases

All available databases can be found at ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/. Information about how to download/install/use databases is provided: README.md.

Databases are pre-built, including the required hash.k2d, opts.k2d, and taxo.k2d files. Each database also includes 100mer, 150mer, and 200mer Bracken files.