This is a KrakenUniq database built using NCBI non-redundant NT / NR records from June 2020 that includes all microbial organisms (archaea,bacteria,viral,fungi,protozoa,parasitic_worms) plus human reference genome and a few complete eukaryotic genomes, 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: 17044/scilifelab.20518251

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-download --db DBDIR --dust microbial-nt
./krakenuniq-download --db DBDIR --taxa "archaea,bacteria,viral,fungi,protozoa,parasitic_worms" --dust --exclude-environmental-taxa nt

module load bioinfo-tools
module load perl
module load jellyfish/1.1.11
./krakenuniq-build --db DBDIR --kmer-len 31 --threads 10 --taxids-for-genomes --taxids-for-sequences
Found jellyfish v1.1.11
Kraken build set to minimize disk writes.
Found 5 sequence files (*.{fna,fa,ffn,fasta,fsa}) in the library directory.
Skipping step 1, k-mer set already exists.
Skipping step 2, no database reduction requested.
Skipping step 3, k-mer set already sorted.
Skipping step 4, seqID to taxID map already complete.
Skipping step 5, taxDB exists.
Building  KrakenUniq LCA database (step 6 of 6)...
 Adding taxonomy IDs for sequences
 Adding taxonomy IDs for genomes
Reading taxonomy index from taxDB. Done.
Getting database0.kdb into memory (370.837 GB) ... Done
Loaded database with 33181953872 keys with k of 31 [val_len 4, key_len 8].
Reading sequence ID to taxonomy ID mapping ... [starting new taxonomy IDs with 1000000001] got 10410911 mappings.
Finished processing 10410911 sequences (skipping 0 empty sequences, and 0 sequences with no taxonomy mapping)
Writing kmer counts to database.kdb.counts...
Writing database from RAM back to database.kdb ...
Writing new TaxDB ...
LCA database created. [19h12m43.636s]
Creating database summary report database.report.tsv ...
/crex/proj/uppstore2018095/private/NBIS_Demo/KrakenUniq/krakenuniq/KrakenUniq/classify -d ././database.kdb -i ././database.idx -t 20 -r database.report.tsv -a ././taxDB -p 12 /dev/fd/63
 Database ././database.kdb
Loaded database with 33181953872 keys with k of 31 [val_len 4, key_len 8].
Reading taxonomy index from ././taxDB. Done.