Dengue antigenic variation and evolutionary dynamics

Titer model

About the titer model

The titer model seeks to assign discrete units of antigenic change to specific mutations across the dengue phylogeny. Full model details can be found in Neher et al. and our preprint.

Running the titer model

This model was originally published in Neher et al (PNAS, 2016) and implemented as part of the Nextstrain augur package. The relevant portions of the repository have been reproduced here under implementation-nextstrain-augur. Documentation, including install instructions, for the full augur pipeline can be found here. Note that for future reuse, I would actually recommend running the model via the newly modularized implementation here.

1 - Prepare input files

dengue.prepare.py handles subsampling and other basic dataset config. You can edit the function make_config here with any desired changes.

cd dengue-antigenic-dynamics/titer_model/implementation-nextstrain-augur/builds/dengue/
python dengue.prepare.py #--options

NB: For this dataset, step 1 has been run for you; see ./implementation-nextstrain-augur/dengue/prepared/titered.json

2 - Run the titer pipeline (and estimate clade frequencies)

dengue.process.py handles the actual analysis; parameter settings, etc. can be changed in the make_config function here.
python dengue.process.py -j path_to_prepared_json

NB: For this dataset, step 2 has been run for you; see ./titered_output/

3 - Check out your results

Results are output in JSON format, found in ./processed/. You can parse and examine results using the notebook found here.