2020/06 UPDATE
All Kraken 2 databases available are located at: ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/.
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:
Pre-built Kraken 2 Databases
The following 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.
- Kraken 2 16S Greengenes 13_5 DB (72.1 MB)
- Kraken 2 16S RDP 11.5 DB (168 MB)
- Kraken 2 16S Silva 132 DB (117 MB)
- Kraken 2 16S Silva 138 DB (112 MB)
These additional databases have been provided by non-CCB labs:
- GTDB_r89_54k linkA collection of database files for use with Centrifuge, Kraken 1, or Kraken 2 that can be used to classify metagenomes using the GTDB_389_54k index. More information and details at: https://github.com/rrwick/Metagenomics-Index-Correction
- Maxikraken2 and Kraken2-microbial databases. These databases are maintained by LomanLab. More information at the link provided.