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Loman Lab Mock Community Experiments

Databases

kraken2-microbial (September 2018, 30GB)

A database built by stacking the kraken2 --download-library command for the following database types:

kraken2 downloads and hashes sequences from RefSeq that are marked as “complete” or “representative”

Prepared 2018-09-03 by @samstudio8

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:

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

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!