CCB » Software » Kraken2

2020/06 UPDATE

All Kraken 2 databases available are located at:

Kraken 2 Code Download

  • Source (99 KB): Kraken2's source code and README. The current official version of Kraken 2 is v2.0.8-beta (released April 25th, 2019). However, additional fixes/changes are in the newest github version.
  • The source code for the current release and the newest version are both available at the Kraken 2 GitHub repository.

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.

  • MiniKraken2_v1_8GB: (5.5GB) 8GB Kraken 2 Database built from the refseq bacteria, archaea, and viral libraries.
  • MiniKraken2_v2_8GB: (5.5GB) 8GB Kraken 2 Database built from the Refseq bacteria, archaea, and viral libraries and the GRCh38 human genome

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

Pre-built Kraken 2 Databases

The following databases can be found at Information about how to download/install/use databases is provided:

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.

These additional databases have been provided by non-CCB labs: