Pipeline components for real-time virus analysis

Lassa build

How to run

  • Run all commands from this directory
python lassa.prepare.py
  • Running lassa.prepare.py creates the files prepared/lassa_s.json and prepared/lassa_l.json.

3. Run build

python lassa.process.py --json prepared/lassa_s.json
python lassa.process.py --json prepared/lassa_l.json

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

4. Copy JSONs to auspice

cp auspice/lassa_* ../../../auspice/data/

5. Run auspice to visualize

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