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Pyro models for SARS-CoV-2 analysis

This repository is described in the paper "Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility". Figures and supplementary data for that paper are in the paper/ directory.

Reproducing

  1. Clone this repo into say ~/pyro-cov
  2. cd ~/pyro-cov
  3. make install # installs dependencies
  4. conda install nodejs
  5. npm install --global @nextstrain/nextclade
  6. Work with GISAID to get a data agreement.
  7. Define environment variables GISAID_USERNAME, GISAID_PASSWORD, and GISAID_FEED
  8. make update # clones other data sources
  9. python mutrans.py --vary-holdout
  10. generate plots by running various jupyter notebooks, e.g. mutrans.ipynb

Installing

make install

or literally

pip install -e .

Citing

If you use this software, please consider citing:

@article {Obermeyer2021.09.07.21263228,
  author = {Obermeyer, Fritz and
            Schaffner, Stephen F. and
            Jankowiak, Martin and
            Barkas, Nikolaos and
            Pyle, Jesse D. and
            Park, Daniel J. and
            MacInnis, Bronwyn L. and
            Luban, Jeremy and
            Sabeti, Pardis C. and
            Lemieux, Jacob E.},
  title = {Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility},
  elocation-id = {2021.09.07.21263228},
  year = {2021},
  doi = {10.1101/2021.09.07.21263228},
  publisher = {Cold Spring Harbor Laboratory Press},
  URL = {https://www.medrxiv.org/content/early/2021/09/13/2021.09.07.21263228},
  eprint = {https://www.medrxiv.org/content/early/2021/09/13/2021.09.07.21263228.full.pdf},
  journal = {medRxiv}
}