Kraken2 Human Pangenome Reference Consortium Release 1 database

A kraken2 database built from the genome assemblies generated in the first release of the Human Pangenome Reference Consortium (https://projects.ensembl.org/hprc/). This archive contains the three files required by kraken2, hash.k2d, opts.k2d, and taxo.k2d, along with inspect.txt, which is obtained by running kraken2-inspect on the database.

The genomes for this database were downloaded using the assembly summary text file included in this dataset and genome_updater.sh (v0.6.3; https://github.com/pirovc/genome_updater)

genome_updater.sh -m -a -f "genomic.fna.gz" -t 8 -e "hprc.r1_assembly_summary.txt" -o HPRC_genomes/

The python script prepare_kraken_fasta.py was then used to prepare the assemblies for use in kraken with the following command

python prepare_kraken_fasta.py -r -T 9606 -o HPRC.fna HPRC_genomes/

The database was then built with kraken2 (v2.1.6) using the following commands

k2 download-taxonomy --db dbk2 add-to-library --db db --threads 8 --file genomes.fna --no-maskingk2 build --db db --no-masking --threads 16k2 clean --db dbk2 inspect --db db > inspect.txt