influenza-override-groups

This directory contains a mapping of Influenza A and Influenza B genbank assemblies to segment accessions, as well as the code to update this mapping.

Mapping files:

• results/197911-groups.json (Influenza A)
• results/11520-groups.json (Influenza B)

Getting Started

After cloning this repository, install dependencies using pixi:

pixi install

Generating these files

Use the pixi tasks to regenerate the grouping files:

# For Influenza A
pixi run regenerate-influenza-a

# For Influenza B
pixi run regenerate-influenza-b

What the script is doing

1. Download the metadata information for the assemblies from genbank and refseq.
2. Hydrate the assemblies, which means that the actual sequence information is downloaded.
3. For each assembly parse the fna file to find the segment names, and store the final JSON file.

For Influenza A, step 1 takes about 3 minutes, step 2 can take around 1 hour, and step 3 should take only 30 seconds.

GitHub Actions to regenerate the grouping files

This repo also has a GitHub action per organism, to regenerate the files. When run, the action creates a PR to update the grouping file. The actions are scheduled to run every night.

How these files are used

Loculus can use these files during ingest, to override groups. You can specify these files in the ingest configuration using the grouping_override setting by pointing directly to the file URL:

grouping_override: "https://GenSpectrum.github.io/influenza-override-groups/results/197911-groups.json"

Acknowledgements

This repo builds on the work in https://github.com/anna-parker/influenza-a-groupings.