PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
See our website: https://www.poppunk.net
Description
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
Installation
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.
Through conda (recommended)
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
Through pip
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
.
Quick usage
See the https://poppunk.readthedocs.io/en/latest/quickstart.html guide for a brief tutorial.