proGenomes-cli

proGenomes-cli is a command-line tool for exploring the proGenomes dataset of bacterial and archaeal genomes.

If you use this software in a publication please cite:

Anthony Fullam, Ivica Letunic, Oleksandr M Maistrenko, Alexandre Areias Castro, Luis Pedro Coelho, Anastasiia Grekova, Christian Schudoma, Supriya Khedkar, Mahdi Robbani, Michael Kuhn, Thomas S B Schmidt, Peer Bork, Daniel R Mende, proGenomes4: providing 2 million accurately and consistently annotated high-quality prokaryotic genomes, Nucleic Acids Research, 2025;, gkaf1208, https://doi.org/10.1093/nar/gkaf1208

Installation

proGenomes-cli can be installed using pip:

pip install progenomes

or using conda through the bioconda channel:

conda install -c bioconda progenomes

Usage

After installation, the progenomes command provides access to several subcommands:

progenomes download <options>   # Download genome data
progenomes view <options>       # Inspect downloaded data

Refer to the built-in help for full details on available commands.

progenomes --help

License

This project is licensed under the MIT License.