poppunk 2.0.1

PopPUNK (POPulation Partitioning Using Nucleotide Kmers)

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 [e-mail]: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.