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. Use custom titer tsv file from Sidney:
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