Pipeline components for real-time virus analysis

Zika build

How to run

1. Run all commands from this directory

2. Download FASTA file via fauna and prepare analysis

python zika.prepare.py

Alternatively, supply a FASTA file with conforming headings and pass in this file with --sequences. python zika.prepare.py --sequences example_data/zika.fasta Running zika.prepare.py creates the file prepared/zika.json.

3. Run build

python zika.process.py

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

4. Copy JSONs to auspice

cp auspice/zika_* ../../../auspice/data/

5. Run auspice to visualize

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