Skip to main content

A python wrapper around DNA k-kmer counter Jellfish

Project description

pyJellyfish : Python wrapper around Jellyfish (k-mer counter)

Python version PyPi version


This install script is not yet PEP517 compliant, which means the wheel and setuptools packages need to be in your environment.

Do not forget this line when setting up your environment (see below):

pip install --upgrade setuptools wheel pip


This tool essentially serves as an installer for Jellyfish for use with Python. A small bundle of utilities is also included.



With pip

python -m venv $HOME/.virtualenvs/km
source $HOME/.virtualenvs/km/bin/activate
pip install --upgrade setuptools wheel pip
pip install .


Additionally, pyJellyfish contains an option to manually specify which Jellyfish version one wishes to build against. This can be done by running with the custom build command jellyfish.

source $HOME/.virtualenvs/km/bin/activate
python jellyfish --version 2.2.10

Note that the setup script will automatically detect if jellyfish has already been built and use that instead of re-running the jellyfish step. After running the previous command, installation will proceed as usual.

pip install .


  • Python 3.6.0 or later

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

pyjellyfish-1.2.0.tar.gz (2.9 MB view hashes)

Uploaded Source

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page