Kraken2 Human Pangenome Reference Consortium database

A kraken2 database built from the genome assemblies used by 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, ktaxonomy.tsv, which contains the taxonomy information of the database (obtained by running https://github.com/jenniferlu717/KrakenTools#make_ktaxonomypy).

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_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 using the following commands

kraken2-build --download-taxonomy --db db/
kraken2-build --add-to-library HPRC.fna --db db/
kraken2-build --build --db db/ --threads 16

本Kraken2（kraken2）数据库基于人类泛基因组参考联盟（Human Pangenome Reference Consortium, HPRC，https://projects.ensembl.org/hprc/）所使用的基因组组装结果构建。该归档文件包含Kraken2运行所需的三个核心文件：hash.k2d、opts.k2d与taxo.k2d，同时附带通过对该数据库执行kraken2-inspect得到的inspect.txt，以及通过运行https://github.com/jenniferlu717/KrakenTools#make_ktaxonomypy 生成的包含数据库分类学信息的ktaxonomy.tsv。

本数据库所用的基因组数据通过本数据集附带的组装汇总文本文件与genome_updater.sh（v0.6.3；https://github.com/pirovc/genome_updater）下载得到，具体执行命令如下：
genome_updater.sh -m -a -f "genomic.fna.gz" -t 8 -e "hprc_assembly_summary.txt" -o HPRC_genomes/

随后使用Python脚本prepare_kraken_fasta.py对基因组组装结果进行预处理，以适配Kraken2的使用需求，所用命令为：
python prepare_kraken_fasta.py -r -T 9606 -o HPRC.fna HPRC_genomes/

最后通过以下命令使用Kraken2完成该数据库的构建：
kraken2-build --download-taxonomy --db db/
kraken2-build --add-to-library HPRC.fna --db db/
kraken2-build --build --db db/ --threads 16