Pipeline components for real-time virus analysis

DENGUE Pipeline Notes

augur/dengue/dengue.py can run either a serotype-specific build or an all-serotype build.

By default, fauna/vdb/dengue_download.py downloads all serotypes together.
fauna$ python vdb/dengue_download.py -db vdb -v dengue
A single serotype can be downloaded like:
fauna$ python vdb/dengue_download.py -db vdb -v dengue --select serotype:1

To run corresponding augur builds:
augur$ python dengue/dengue.py -s all (default)
augur$ python dengue/dengue.py -s denv1

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.

rejig status

  • basic prepare / process working
  • titers: NO
  • frequencies: NO
cd dengue
rm prepared/* auspice/* processed/*
python dengue.prepare.py -s <SEROTYPE>
python dengue.process.py -j <prepared/JSON>