kmhelpers

A Python toolkit for managing, compressing, and querying kmindex indices efficiently.

Documentation: https://sebllns.github.io/kmhelpers/

Table of Contents

• Disclaimers
• Getting Started
• Documentation
• License
• Contact
• Changelog
• Acknowledgements

Disclaimers

kmhelpers is provided "as is", without warranty (see LICENSE). Operations that build, update, or compress indices modify data in place, so it might be useful to back up important data beforehand, and if you are not sure of something, ask here before running it.

Getting started

Clone the repository and navigate to it

git clone https://github.com/sebllns/kmhelpers
cd kmhelpers

To clone a released version directly:

git clone --branch vX.Y.Z https://github.com/sebllns/kmhelpers
cd kmhelpers

Quick Install with Conda

This will automatically:

• Install kmhelpers Python package
• Install kmindex and ntcard

Prerequisites: Conda (Miniconda or Anaconda) must be installed. If you don't have it, see Installation Instructions.

# Create environment with kmindex pre-installed
conda env create -f conda/environment.yml -p ./.env

# Activate the environment
# Run this each time you open a new terminal session before using kmhelpers
conda activate ./.env

Note: Once per terminal session, activate the environment before using kmhelpers:

conda activate /path/to/kmhelpers/.env

.env can be replaced by any path, for example a shared or permanent location like ~/.kmhelpers:

conda env create -f conda/environment.yml -p ~/.kmhelpers
conda activate ~/.kmhelpers

Verify Installation

Once the environment has been activated:

# Check the installed version
kmhelpers --version

# View available commands
kmhelpers --help

Tip: kh is available as a short alias for kmhelpers (e.g. kh --help).

# Check ntcard
ntcard --version

# Check kmtricks
kmtricks --version

# Check kmindex
kmindex --version

Update

To pull the latest changes from the default branch (main):

git pull origin main

To check out a released version instead:

git fetch --tags
git checkout vX.Y.Z

If your local branch is already tracking a remote branch, you can simply run:

git pull

Check the installed version:

kmhelpers --version

Documentation

https://sebllns.github.io/kmhelpers/

Covers installation, a full tutorial, command reference, core concepts, and the API reference.

License

This project is licensed under the GNU General Public License - see the LICENSE file for details.

Copyright (c) 2026 Sébastien Bellenous, Genscale, INRIA

Contact

For questions, bug reports, or contributions, please contact:

• Author: Sébastien BELLENOUS
• Email: kmhelpers@groupes.renater.fr
• Repository: GitHub
• Supervisor: Pierre Peterlongo

Version: 0.7.0 Status: Development

Changelog

See CHANGELOG.md for detailed version history.

Acknowledgements

The authors thank Téo Lemane for developing kmindex and for his responsiveness in addressing feature requests and issues raised during the development of kmhelpers. We acknowledge the GenOuest core facility (https://www.genouest.org) for providing the computing infrastructure. The work was funded by the Inria Challenge "OmicFinder" (https://project.inria.fr/omicfinder/), and by the state funding managed by the French National Research Agency under the France 2030 program [ANR-22-PEAE-0005].