Installation

pip install kraken-db-builder

Usage

kdb --help

kraken-db-builder --help

To create standard Kraken2 database

kdb --db-type standard

Before creating a standard database, you can try a smaller database like fungi.

kdb --db-type fungi

To use locally downloaded files, run the following command

kdb --db-name k2_test --genomes-dir /path/to/genomes --taxonomy-dir /path/to/taxonomy

To limit the number of genomes in the database, use the --limit option

kdb --db-name k2_test_100 --genomes-dir /path/to/genomes --limit 1000

Why kdb(kraken-db-builder)?

kdb was aimed to created to provide a simple and easy to use tool to build wide variety of databases with a single command.

Why not kraken2-build?

kraken2-build is a tool provided by Kraken2 to build Kraken2 database. It is a great tool but it is limited to build only Kraken2 database. kdb is a more generic tool which can be used to build databases for Kraken2, Centrifuge, Bracken, etc.

Documentation

• Kraken2 Database Builder
• Mastering Kraken2