See our website: https://www.poppunk.net

See the documentation and the paper.

If you find PopPUNK useful, please cite us:

Lees JA, Harris SR, Tonkin-Hill G, Gladstone RA, Lo SW, Weiser JN, Corander J, Bentley SD, Croucher NJ. Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome Research 29:304-316 (2019). doi:10.1101/gr.241455.118

This is for the command line version. For more details see installation in the documentation.

There are other interfaces, in-browser and through galaxy, detailed here.

The easiest way is through conda, which is most easily accessed by first installing miniconda. PopPUNK can then be installed by running:

conda install poppunk

If the package cannot be found you will need to add the necessary channels:

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

If you do not have conda you can also install through pip:

python3 -m pip install poppunk

You will need to be using Python 3.

Using both of these methods command poppunk will then be directly executable. Alternatively clone this repository:

git clone git@github.com:johnlees/PopPUNK.git

Then run with python poppunk-runner.py.

See the https://poppunk.readthedocs.io/en/latest/quickstart.html guide for a brief tutorial.