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
You can also run your command with --citation to get a list of citations and a
suggested methods paragraph.
News
2021-03-15
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.
2020-09-30
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.pyon your.dists.pklfile and re-run model fits. - Create the database with
poppunk_sketchdirectly, rather thanPopPUNK --create-db
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
Quick usage
See the quickstart guide for a brief tutorial.
Release files for poppunk 2.4.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| poppunk-2.4.0.tar.gz | 1.3 MB | Details |
Release files / poppunk-2.4.0.tar.gz
| Download URL | poppunk-2.4.0.tar.gz |
|---|---|
| Size | 1.3 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
3cc055e5db1f18cf95141adf297b0e396900e7084810f0808766bfd7b76855bd
|
|
BLAKE2b-256 checksum How to use checksums |
7539f49a16561bed8224b9ec75a3df6a9cb3f6a24981789a17e73ccc2ce26e38
|
| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/3.4.1 importlib_metadata/3.7.3 pkginfo/1.7.0 requests/2.25.1 requests-toolbelt/0.9.1 tqdm/4.59.0 CPython/3.8.8
|
