Poppunk2 lineage assignment

About

This tool takes a pre-built Poppunk2 cluster database and links novel genomes to the most similar cluster. Note that it does not update or otherwise modify the clusters, and so provides a stable lineage assignment tool

Supported species

Species	Creator
Vibrio cholerae	Vibriowatch
Streptococcus pneumoniae	GPS

How to build

1. NB. Update versions.json with the current version of PopPUNK2 in anaconda.
2. Update the scheme metadata if any files have changed.
3. Run docker build, specifying the library as a build argument, e.g for V. cholerae:

docker build --pull --rm --build-arg LIBRARY=vibriowatch -t registry.gitlab.com/cgps/pathogenwatch/analyses/poppunk2:v1.1.0-666

How to add a new schema

1. Create a new set of clusters using poppunk2.
2. Place the required files in a directory - use gpsc_db as a template.
3. Create a new metadata.json file like one of the examples.

Example scheme metadata file

{
  "email": "vibriowatch@sanger.ac.uk",
  "label": "VC",
  "source": "Vibriowatch clusters",
  "url": "https://vibriowatch.readthedocs.io/en/latest/mlst.html#how-to-view-poppunk-information-for-your-isolate",
  "versions": {
    "scheme": "v1"
  }
}

Scheme-specific notes

GPSC (Streptococcus pneumoniae)

• Releases are triggered on receipt of an email announcing an update from the GPS.
• Download links take the following formats:
  • https://gps-project.cog.sanger.ac.uk/GPS_v8_ref.tar.gz
  • https://gps-project.cog.sanger.ac.uk/GPS_v8_external_clusters.csv