Main tool :
Additional tools:
- biopython 1.83
- pp-sketchlib 2.1.2
- python 3.10.13
- rapidnj 2.3.2
- treeswift 1.1.39
Full documentation: https://poppunk.readthedocs.io/en/latest/
PopPUNK is also available as a webtool: https://www.poppunk.net/
PopPUNK is a tool for clustering genomes.
NOTE: This docker image is intended for the CLI usage of the PopPUNK tool. It has not been built with the full web-interface functionality in mind.
This example is for usage of PopPUNK for Streptococcus pneumoniae clustering using a database & reference files provided by the Global Pneumococcal Sequencing Project. An example S. pneumoniae genome can be obtained from here
# poppunk requires an input File Of File Names (FOFN). headerless TSV with a sample name (first column), followed by path to input FASTA
$ echo -e "SRR2912551\t/data/SRR2912551.fna.gz" > poppunk_input.tsv
# showing reference files, FASTA input, and poppunk_input.tsv
$ ls
GPS_v6/ GPS_v6_external_clusters.csv SRR2912551.fna.gz poppunk_input.tsv
# run the docker container interactively
# followed by poppunk command run inside the container
$ docker run --rm -ti -v ${PWD}:/data -u $(id -u):$(id -g) staphb/poppunk:2.6.2
$ poppunk_assign --db GPS_v6 --distances GPS_v6/GPS_v6.dists --query /data/poppunk_input.tsv --output docker_test --external-clustering GPS_v6_external_clusters.csv
PopPUNK: assign
(with backend: sketchlib v2.0.0
sketchlib: /opt/conda/envs/poppunk-env/lib/python3.10/site-packages/pp_sketchlib.cpython-310-x86_64-linux-gnu.so)
Graph-tools OpenMP parallelisation enabled: with 1 threads
Mode: Assigning clusters of query sequences
Loading previously refined model
Completed model loading
Sketching 1 genomes using 1 thread(s)
Progress (CPU): 1 / 1
Writing sketches to file
WARNING: versions of input databases sketches are different, results may not be compatible
Calculating distances using 1 thread(s)
Progress (CPU): 100.0%
Selected type isolate for distance QC is 10050_2#1
Network loaded: 42163 samples
Done