Pipeline components for real-time virus analysis

Seasonal flu (H3N2, H1N1pdm, B/Vic, B/Yam) build


  • all lineages working
  • references only defined for HA (so far)
  • subsampling is always a single pass and cannot be repeated
  • tree frequencies have not been tested properly
  • matchClades has not been properly tested

summary of the necessary files

flu.prepare.pyPrepare script.
flu.process.pyProcess script.
flu_info.pyHolds (a lot of) information about sequences to drop, reference genomes etc. Used by prepare.
../../fauna/flu_<SERO>_<SEG>.fasta(Fauna) fasta file
colors.flu.tsvcolor maps

How to run

1. Run all commands from this directory

2. Download FASTA file via fauna and prepare analysis

python flu.prepare.py --lineage h3n2 --resolution 3y

Running this creates the file prepared/flu_h3n2_ha_3y.json.

3. Run build

python flu.process.py --json prepared/flu_h3n2_ha_3y.json

This creates intermediary files in processed/ and auspice-ready JSONs in auspice/.

4. Copy JSONs to auspice

cp auspice/flu_* ../../../auspice/data/

5. Run auspice to visualize

cd ../../../auspice
npm run start:local

How to run (batch)

The script run_flu.py will batch calls to flu.prepare.py and flu.process.py to run all combinations of lineage (h3n2, h1n1pdm, vic, yam) and resolution (2y, 3y, 6y, 12y). python run_flu.py