PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
POPulation Partitioning Using Nucleotide Kmers
See our website: https://www.poppunk.net
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
--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
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:
.dists.pklfile and re-run model fits.
- Create the database with
poppunk_sketchdirectly, rather than
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
See the quickstart guide for a brief tutorial.
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