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PopPUNK (POPulation Partitioning Using Nucleotide Kmers)

Project description

POPulation Partitioning Using Nucleotide Kmers

Dev build Status Run tests Documentation Status Anaconda package PyPI version

See our website:


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

You can also run your command with --citation to get a list of citations and a suggested methods paragraph.



We have fixed a number of bugs with may affect the use of poppunk_assign with --update-db. We have also fixed a number of bugs with GPU distances. These are 'advanced' features and are not likely to be encountered in most cases, but if you do wish to use either of these features please make sure that you are using PopPUNK >=v2.4.0 with pp-sketchlib >=v1.7.0.


We have discovered a bug affecting the interaction of pp-sketchlib and PopPUNK. If you have used PopPUNK >=v2.0.0 with pp-sketchlib <v1.5.1 label order may be incorrect (see issue #95).

Please upgrade to PopPUNK >=v2.2 and pp-sketchlib >=v1.5.1. If this is not possible, you can either:

  • Run scripts/ on your .dists.pkl file and re-run model fits.
  • Create the database with poppunk_sketch directly, rather than PopPUNK --create-db


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

Quick usage

See the quickstart guide for a brief tutorial.

Project details

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Source Distribution

poppunk-2.4.0.tar.gz (1.3 MB view hashes)

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