Installation

pip install taxaforge

Usage

taxaforge --help

To create standard Kraken2 database

taxaforge build --db-type standard

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

taxaforge build --db-type fungi

To build a ganon2 database instead, pass --tool ganon2

taxaforge build --tool ganon2 --db-type fungi

To use locally downloaded files, run the following command

taxaforge build --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

taxaforge build --db-name k2_test_100 --genomes-dir /path/to/genomes --limit 1000

Config

Read/write config, stored in the OS default config location (~/.config/taxaforge/config.ini on Linux, ~/Library/Application Support/taxaforge/config.ini on macOS).

taxaforge config set threads 8
taxaforge config get threads
taxaforge config

Why TaxaForge?

TaxaForge aims to provide a simple and easy to use tool to build wide variety of taxonomic classifier databases with a single command.

Why not kraken2-build/ganon directly?

kraken2-build and ganon each build databases for their own tool only. TaxaForge wraps the shared download/taxonomy pipeline once and dispatches to the right tool via --tool, so adding support for more classifiers is a matter of plugging in a new build step.

Documentation

• Kraken2 Database Builder
• Mastering Kraken2