{"id":23757883,"url":"https://github.com/broadinstitute/pyro-cov","last_synced_at":"2025-10-12T04:31:04.200Z","repository":{"id":37266058,"uuid":"292037402","full_name":"broadinstitute/pyro-cov","owner":"broadinstitute","description":"Pyro models of SARS-CoV-2 variants","archived":false,"fork":false,"pushed_at":"2024-07-26T14:29:47.000Z","size":444800,"stargazers_count":78,"open_issues_count":12,"forks_count":30,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-01-22T04:06:04.622Z","etag":null,"topics":["epidemiology","genetics","sars-cov-2"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/broadinstitute.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2020-09-01T15:34:42.000Z","updated_at":"2024-12-17T15:58:45.000Z","dependencies_parsed_at":"2023-02-08T14:30:30.843Z","dependency_job_id":"c03aa338-81ef-4b09-aba9-d2da0018ab45","html_url":"https://github.com/broadinstitute/pyro-cov","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/broadinstitute%2Fpyro-cov/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/broadinstitute","download_url":"https://codeload.github.com/broadinstitute/pyro-cov/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":236130916,"owners_count":19099712,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["epidemiology","genetics","sars-cov-2"],"created_at":"2024-12-31T19:51:47.826Z","updated_at":"2025-10-12T04:30:56.369Z","avatar_url":"https://github.com/broadinstitute.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Github Release](https://img.shields.io/github/v/release/broadinstitute/pyro-cov)](https://github.com/broadinstitute/pyro-cov/releases)\n[![DOI](https://zenodo.org/badge/292037402.svg)](https://zenodo.org/badge/latestdoi/292037402)\n\n# Pyro models for SARS-CoV-2 analysis\n\n![Overview](paper/schematic_overview.png)\n\nSupporting 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.\n\nThis 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).\n\n## Reproducing\n\n### Install software\n\nClone this repository:\n```sh\ngit clone git@github.com:broadinstitute/pyro-cov\ncd pyro-cov\n```\n\nInstall this python package:\n```py\npip install -e .\n```\n\n### Get access to GISAID data\n\nWork with GISAID to get a data agreement.\nDefine the following environment variables:\n```\nGISAID_USERNAME\nGISAID_PASSWORD\nGISAID_FEED\n```\nFor example my username is `fritz` and my gisaid feed is `broad2`.\n\n### Download data\nThis downloads data from GISAID and clones repos for other data sources.\n```sh\nmake update\n```\n\n### Preprocess data\n\nThis takes under an hour.\nResults are cached in the `results/` directory, so re-running on newly pulled data should be able to re-use alignment and PANGOlineage classification work.\n```sh\nmake preprocess\n```\n\n### Analyze data\n```sh\nmake analyze\n```\n\n### Generate plots and tables\nPlots and tables are generated by running various notebooks:\n- [mutrans.py](notebooks/mutrans.ipynb)\n- [mutrans_backtesting.py](notebooks/mutrans_backtesting.ipynb)\n- [mutrans_gene.ipynb](notebooks/mutrans_gene.ipynb)\n\n## Citing\n\nIf you use this software or predictions in the [paper](paper/) directory please consider citing:\n\n```\n@article {Obermeyer2021.09.07.21263228,\n  author = {Obermeyer, Fritz and\n            Schaffner, Stephen F. and\n            Jankowiak, Martin and\n            Barkas, Nikolaos and\n            Pyle, Jesse D. and\n            Park, Daniel J. and\n            MacInnis, Bronwyn L. and\n            Luban, Jeremy and\n            Sabeti, Pardis C. and\n            Lemieux, Jacob E.},\n  title = {Analysis of 2.1 million SARS-CoV-2 genomes identifies mutations associated with transmissibility},\n  elocation-id = {2021.09.07.21263228},\n  year = {2021},\n  doi = {10.1101/2021.09.07.21263228},\n  publisher = {Cold Spring Harbor Laboratory Press},\n  URL = {https://www.medrxiv.org/content/early/2021/09/13/2021.09.07.21263228},\n  eprint = {https://www.medrxiv.org/content/early/2021/09/13/2021.09.07.21263228.full.pdf},\n  journal = {medRxiv}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fpyro-cov","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbroadinstitute%2Fpyro-cov","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbroadinstitute%2Fpyro-cov/lists"}