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