Roadmap#

This document describes our future plans for additions to PopPUNK, pp-sketchlib and BeeBOP and BeeBOP. Tasks are in order of priority.

PopPUNK#

  1. Containerise the workflow. See #193, #277, #278.

  2. Add full worked tutorials back to the documentation #275.

  3. Make the update pipeline more robust. See #273.

  4. Codebase optimsation and refactoring

    • Modularisation of the network code #249.

    • Removing old functions #103

  5. Add more species databases:

  6. Stable names for lineage/subclustering modes.

Other enhancements listed on the issue page are currently not planned.

pp-sketchlib#

  1. Update installation in package managers

    • Update for new macOS #92

    • Rebuild conda recipe for CUDA12 and newer HDF5 #46

  2. Allow amino-acids as input #89.

Other enhancements listed on the issue page are currently not planned.

BeeBOP#

  1. Update backend database to v8 #42.

  2. Update CI images.

  3. Add more info on landing page.

    • News page.

    • About page.

    • Methods description.

  4. Add custom cluster names (e.g. GPSCs)

  5. Integration tests for error logging.

  6. Persist user data.

    • Persist microreact tokens #41.

    • Allow user to change or delete tokens

  7. Add linage/subclusters to results page #23.

  8. Report sample quality to user.

  9. Front-end update for large numbers of input files.

  10. Add serotype prediction for S. pneumoniae.

  11. Add multiple species databases.