This is a KrakenUniq database built using NCBI RefSeq https://ftp.ncbi.nlm.nih.gov/refseq/release/ complete genomes records from May 2020 that includes all microbial organisms (archaea,bacteria,viral,fungi,protozoa,parasitic_worms), for the full list of orgnisms included into the database please see library-files.txt. 

The KrakenUniq database was built by Nikolay Oskolkov, Lund University, within the NBIS SciLifeLab long-term support project, PI Anders Götherström, Centre for Palaeogenetics (CPG), Stockholm, Sweden. 

DOI: 10.17044/scilifelab.21299541

For questions regarding the database please use Nikolay.Oskolkov@biol.lu.se or nikolay.oskolkov@scilifelab.se

The database was build using KrakenUniq version 0.5.8.

For details of database building, please see database-build.log as well as the command lines below:

$KRAKENUNIQ_PATH/krakenuniq-download --db DBDIR_MICROBE taxonomy
$KRAKENUNIQ_PATH/krakenuniq-download --db DBDIR_MICROBE --threads 10 --dust refseq/bacteria refseq/archaea refseq/viral refseq/fungi refseq/protozoa refseq/parasitic_worms
$PATH_TO_KRAKENUNIQ/./krakenuniq-build --db DBDIR_MICROBE --kmer-len 31 --threads 20 --taxids-for-genomes --taxids-for-sequences

If you use the KrakenUniq databases and Bowtie2 indexes for you research we kindly ask you to cite our work here https://www.biorxiv.org/content/10.1101/2022.10.03.510579v1. doi: https://doi.org/10.1101/2022.10.03.510579
Please contact Nikolay Oskolkov if you discover any problems downloading or using the databases.