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
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/poppunk_pickle_fix.py
on your.dists.pkl
file and re-run model fits. - Create the database with
poppunk_sketch
directly, rather thanPopPUNK --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.
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
See the quickstart guide for a brief tutorial.