Pipeline components for real-time virus analysis

Dengue build

Can run either a serotype-specific build or an all-serotype build.

N.B.: By default, serotype-specific builds use the respective reference genomes specified by LANL. The all-serotype build uses the reference genome from serotype 4.

How to run

1. Run all commands from this directory

2. Download sequence FASTAs file via fauna

Requires 5 FASTAs (dengue_all.fasta, dengue_denv1.fasta, dengue_denv2.fasta, dengue_denv3.fasta and dengue_denv4.fasta).

3. Download titer tsv file via fauna

Requires dengue_titers.tsv.

4. Prepare analysis

python dengue.prepare.py

Running dengue.prepare.py creates the files prepared/dengue_all.json, prepared/dengue_denv1.json, etc...

5. Run build

python dengue.process.py

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

6. Copy JSONs to auspice

cp auspice/dengue_* ../../../auspice/data/

7. Run auspice to visualize

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