https://github.com/broadinstitute/pyro-cov
Pyro models of SARS-CoV-2 variants
https://github.com/broadinstitute/pyro-cov
epidemiology genetics sars-cov-2
Last synced: 8 months ago
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Pyro models of SARS-CoV-2 variants
- Host: GitHub
- URL: https://github.com/broadinstitute/pyro-cov
- Owner: broadinstitute
- License: apache-2.0
- Created: 2020-09-01T15:34:42.000Z (about 5 years ago)
- Default Branch: master
- Last Pushed: 2024-07-26T14:29:47.000Z (about 1 year ago)
- Last Synced: 2025-01-22T04:06:04.622Z (9 months ago)
- Topics: epidemiology, genetics, sars-cov-2
- Language: Jupyter Notebook
- Homepage:
- Size: 424 MB
- Stars: 78
- Watchers: 15
- Forks: 30
- Open Issues: 12
-
Metadata Files:
- Readme: README.md
- Contributing: CONTRIBUTING.md
- License: LICENSE
Awesome Lists containing this project
README
[](https://github.com/broadinstitute/pyro-cov/releases)
[](https://zenodo.org/badge/latestdoi/292037402)
# Pyro models for SARS-CoV-2 analysis
Supporting material for the paper ["Analysis of 6.4 million SARS-CoV-2 genomes identifies mutations associated with fitness"](https://www.science.org/doi/10.1126/science.abm1208) ([medRxiv](https://www.medrxiv.org/content/10.1101/2021.09.07.21263228v2)). Figures and supplementary data for that paper are in the [paper/](paper/) directory.
This is open source, but we are not intending to support code for use by outside groups. To use outputs of this model, we recommend ingesting the tables [strains.tsv](paper/strains.tsv) and [mutations.tsv](paper/mutations.tsv).
## Reproducing
### Install software
Clone this repository:
```sh
git clone git@github.com:broadinstitute/pyro-cov
cd pyro-cov
```
Install this python package:
```py
pip install -e .
```
### Get access to GISAID data
Work with GISAID to get a data agreement.
Define the following environment variables:
```
GISAID_USERNAME
GISAID_PASSWORD
GISAID_FEED
```
For example my username is `fritz` and my gisaid feed is `broad2`.
### Download data
This downloads data from GISAID and clones repos for other data sources.
```sh
make update
```
### Preprocess data
This takes under an hour.
Results are cached in the `results/` directory, so re-running on newly pulled data should be able to re-use alignment and PANGOlineage classification work.
```sh
make preprocess
```
### Analyze data
```sh
make analyze
```
### Generate plots and tables
Plots and tables are generated by running various notebooks:
- [mutrans.py](notebooks/mutrans.ipynb)
- [mutrans_backtesting.py](notebooks/mutrans_backtesting.ipynb)
- [mutrans_gene.ipynb](notebooks/mutrans_gene.ipynb)
## Citing
If you use this software or predictions in the [paper](paper/) directory 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}
}
```