kraken2-microbial (September 2018, 30GB)
A database built by stacking the kraken2 --download-library command for the following database types:
- archaea
- bacteria
- fungi
- protozoa
- viral
- UniVec_Core
kraken2 downloads and hashes sequences from RefSeq that are marked as “complete” or “representative”
Prepared 2018-09-03 by @samstudio8
hash.k2d(30 GB,b327a46e5f8122c6ce627aecf13ae5b1)opts.k2d(48 B,e77f42c833b99bf91a8315a3c19f83f7)taxo.k2d(1.7 MB,764fee20387217bd8f28ec9bf955c484)
mkdir kraken2-microbial-fatfree/
cd kraken2-microbial-fatfree/
wget -c https://refdb.s3.climb.ac.uk/kraken2-microbial/hash.k2d
wget https://refdb.s3.climb.ac.uk/kraken2-microbial/opts.k2d
wget https://refdb.s3.climb.ac.uk/kraken2-microbial/taxo.k2d
Note wget -c will allow you to continue a stalled download without starting over!
maxikraken2_1903_140GB (March 2019, 140GB)
A database built in a similar way to kraken2-microbial, but instead allowing hashes to be generated from genomes that are not “complete” or “representative”, for the following database types:
- archaea
- bacteria
- fungi
- protozoa
- viral
- human
The database has been made available for sharing by Daniel Fischer (Natural Resources Institute Finland) and was built using scripts available on Github. CSC - IT Center for Science, Finland, is acknowledged for computational resources.
Prepared 2019-03 by @fischuu
hash.k2d(141 GB,0ef062f3dae7f497fe258f67c2e542fe)opts.k2d(48 B,e77f42c833b99bf91a8315a3c19f83f7)taxo.k2d(5.2 MB,f6591859824de9d1893002d5e8d1eee0)
mkdir maxikraken2_1903_140GB/
cd maxikraken2_1903_140GB/
wget -c https://refdb.s3.climb.ac.uk/maxikraken2_1903_140GB/hash.k2d
wget https://refdb.s3.climb.ac.uk/maxikraken2_1903_140GB/opts.k2d
wget https://refdb.s3.climb.ac.uk/maxikraken2_1903_140GB/taxo.k2d
Note wget -c will allow you to continue a stalled download without starting over!