Citing PopPUNK

If you use PopPUNK, PopPIPE or pp-sketchlib in a scientific paper, we would appreciate a citation. As a minimum, please cite the following paper(s):

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 29:1-13 (2019). doi:10.1101/gr.241455.118

Generating citations and methods

You can add --citation to your PopPUNK command to generate a full list of papers to cite. This will also produce a basic methods paragraph for you to edit and include. You can do this after running poppunk_assign or poppunk --fit-model:

poppunk --citation --fit-model bgmm --ref-db example_db --K 4

gives:

We built a database of 28 isolates using pp-sketchlib version 1.7.0 (doi:10.5281/zenodo.4531418) with sketch version 88ee3ff83ba294c928505f991e20078691ed090e, k-mer lengths 13-28, a sketch size of 9984 and dense seeds [6-8]. We assigned variable-length-k-mer clusters (VLKCs) using PopPUNK version 2.4.0 (doi:10.1101/gr.241455.118) by fitting a BGMM with 4 components [1-5].

or:

poppunk_assign --citation --query some_queries.txt --db example_db

gives:

We queried a database of 28 isolates and their pre-assigned variable-length-k-mer clusters (VLKCs) using pp-sketchlib version 1.7.0 (doi:10.5281/zenodo.4531418) with sketch version 88ee3ff83ba294c928505f991e20078691ed090e, k-mer lengths 13-28, a sketch size of 9984 and dense seeds [6-8]. We assigned the VLKCs using PopPUNK version 2.4.0 (doi:10.1101/gr.241455.118) [1-5].

If your journal requires versions for all software packages, you may find running conda list helpful. The poppunk_db_info.py script (Viewing information about a database) can be run on your .h5 files to give useful information too.