Covariants
Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.
Install / Use
/learn @hodcroftlab/CovariantsREADME
<h1 id="covariants" align="center">
CoVariants
</h1>
<p align="center"> <a target="_blank" href="https://covariants.org"> <img height="50px" src="https://img.shields.io/badge/%F0%9F%8C%8D%20Visit%20covariants.org-%23aaaaaa.svg" alt="Visit covariants.org" /> </a> </p> <p align="center"> <a target="_blank" href="https://covariants.org"> <img width="100%" height="auto" src="docs/covariants.gif" alt="An animated screen capture of the website covariants.org, showcasing the user interface and various pages" /> </a> </p>
<h3 id="citation" align="center"> 📜️ Citation </h3>
<p align="center"> <a href="web/package.json"> <img src="https://img.shields.io/github/package-json/v/hodcroftlab/covariants/master/web?label=version&logo=npm" alt="package.json version" /> </a> <a target="_blank" href="https://github.com/hodcroftlab/covariants/blob/master/LICENSE"> <img src="https://img.shields.io/github/license/hodcroftlab/covariants" alt="License" /> </a> </p> <p align="center"> <a target="_blank" href="https://covariants.org/"> <img src="https://img.shields.io/website?url=https%3A%2F%2Fcovariants.org&logo=circle&logoColor=white&label=covariants.org" /> </a> <a target="_blank" href="https://nextstrain:nextstrain@master.covariants.org/"> <img src="https://img.shields.io/website?url=https%3A%2F%2Fnextstrain%3Anextstrain%40master.covariants.org&logo=circle&logoColor=white&label=master.covariants.org" /> </a> </p> <p align="center"> <a href="https://github.com/hodcroftlab/covariants/commits"> <img src="https://img.shields.io/github/last-commit/hodcroftlab/covariants?logo=github" alt="GitHub last commit" /> </a> <a href="https://github.com/hodcroftlab/covariants/commits"> <img src="https://img.shields.io/github/commit-activity/m/hodcroftlab/covariants" alt="GitHub commit activity" /> </a> <a href="https://github.com/hodcroftlab/covariants/graphs/contributors"> <img src="https://img.shields.io/github/contributors/hodcroftlab/covariants?logo=github&label=contributors" alt="GitHub contributors" /> </a> </p> <p align="center"> <a href="docs/Contributing.md"> <img src="https://img.shields.io/badge/contributions-are%20welcome-%234295f5.svg" alt="Contributions: welcome" /> </a> </p>
<h3 id="contributing" align="center"> 🤝 Contributing </h3>
<h3 id="contributors" align="center"> ✨ Contributors </h3>
<h3 align="center"> SARS-CoV-2 Mutations and Variants of Interest </h3> <p align="center"> by Emma B. Hodcroft </p> <p align="center"> <small>Institute of Social and Preventive Medicine</small> <small>University of Bern, Bern, Switzerland</small> <small>& SIB Swiss Insitute of Bioinformatics, Switzerland</small></br> </p>
<p align="center"> <a target="_blank" href="https://covariants.org"> <img height="50px" src="https://img.shields.io/badge/%F0%9F%8C%8D%20Visit%20covariants.org-%23aaaaaa.svg" alt="Visit covariants.org" /> </a> </p> <p align="center"> <a target="_blank" href="https://covariants.org"> <img width="100%" height="auto" src="docs/covariants.gif" alt="An animated screen capture of the website covariants.org, showcasing the user interface and various pages" /> </a> </p>
<h3 id="citation" align="center"> 📜️ Citation </h3>
Emma B. Hodcroft. 2021. "CoVariants: SARS-CoV-2 Mutations and Variants of Interest." https://covariants.org/
<p align="center"> <a href="web/package.json"> <img src="https://img.shields.io/github/package-json/v/hodcroftlab/covariants/master/web?label=version&logo=npm" alt="package.json version" /> </a> <a target="_blank" href="https://github.com/hodcroftlab/covariants/blob/master/LICENSE"> <img src="https://img.shields.io/github/license/hodcroftlab/covariants" alt="License" /> </a> </p> <p align="center"> <a target="_blank" href="https://covariants.org/"> <img src="https://img.shields.io/website?url=https%3A%2F%2Fcovariants.org&logo=circle&logoColor=white&label=covariants.org" /> </a> <a target="_blank" href="https://nextstrain:nextstrain@master.covariants.org/"> <img src="https://img.shields.io/website?url=https%3A%2F%2Fnextstrain%3Anextstrain%40master.covariants.org&logo=circle&logoColor=white&label=master.covariants.org" /> </a> </p> <p align="center"> <a href="https://github.com/hodcroftlab/covariants/commits"> <img src="https://img.shields.io/github/last-commit/hodcroftlab/covariants?logo=github" alt="GitHub last commit" /> </a> <a href="https://github.com/hodcroftlab/covariants/commits"> <img src="https://img.shields.io/github/commit-activity/m/hodcroftlab/covariants" alt="GitHub commit activity" /> </a> <a href="https://github.com/hodcroftlab/covariants/graphs/contributors"> <img src="https://img.shields.io/github/contributors/hodcroftlab/covariants?logo=github&label=contributors" alt="GitHub contributors" /> </a> </p> <p align="center"> <a href="docs/Contributing.md"> <img src="https://img.shields.io/badge/contributions-are%20welcome-%234295f5.svg" alt="Contributions: welcome" /> </a> </p>
<h3 id="contributing" align="center"> 🤝 Contributing </h3>
The code used to generate data seen on CoVariants.org can be found in this repository, mostly in the scripts/ folder, and the code for the web application is in web/.
See Contributors Guide for more details.
<h3 id="terms-of-use" align="center"> 📎 Terms of use </h3>If you use this resource, or its derivatives, including data, code, screenshots an other, please do ensure you add credit in form of citation and/or link back to https://covariants.org
This work is enabled by data made available on GISAID. See the GISAID Terms of Use for more information about how this data can be used. Note that under the terms of use, data on GISAID cannot be redistributed.
This works is closely related to the Nextstrain project and uses Nexstrain builds and resulting data.
<h3 id="license" align="center"> ⚖️ License </h3>Code and work: <a target="_blank" rel="noopener noreferrer" href="LICENSE.md" alt="License file">GNU AFFERO GENERAL PUBLIC LICENSE</a>
CoVariants</br> Copyright 2020-2021 Emma Hodcroft</br>
Screenshots: <a href="https://creativecommons.org/licenses/by/4.0/">CC-BY-4.0</a>
<h3 id="contributors" align="center"> ✨ Contributors </h3>
CoVariants is maintained by
<p align="center"> <p align="center"> <a href="https://github.com/emmahodcroft"> <img src="https://avatars.githubusercontent.com/u/14290674?s=100&u=e074280fd3dd9a9b0e583af5f17d3a69f3068f8b&v=4" width="100px;" alt=""/> </a> </p> <p align="center"> <p align="center"> <a href="https://github.com/emmahodcroft"> Emma B. Hodcroft </a> </p> <p align="center"> <small>Institute of Social and Preventive Medicine</small></br> <small>University of Bern, Bern, Switzerland</small></br> <small>& SIB Swiss Insitute of Bioinformatics, Switzerland</small></br> </p> </p> </p>We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or otherwise. Thanks goes to these wonderful people (emoji key):
<!-- ALL-CONTRIBUTORS-LIST:START - Do not remove or modify this section --> <!-- prettier-ignore-start --> <!-- markdownlint-disable --> <table> <tr> <td align="center"><a href="https://github.com/ivan-aksamentov"><img src="https://avatars0.githubusercontent.com/u/9403403?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Ivan Aksamentov</b></sub></a><br /><a href="https://github.com/hodcroftlab/covariants/commits?author=ivan-aksamentov" title="Code">💻</a> <a href="#infra-ivan-aksamentov" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="https://github.com/hodcroftlab/covariants/commits?author=ivan-aksamentov" title="Documentation">📖</a> <a href="#design-ivan-aksamentov" title="Design">🎨</a></td> <td align="center"><a href="https://github.com/rneher"><img src="https://avatars3.githubusercontent.com/u/8379168?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Richard Neher</b></sub></a><br /><a href="https://github.com/hodcroftlab/covariants/commits?author=rneher" title="Code">💻</a> <a href="#data-rneher" title="Data">🔣</a> <a href="#content-rneher" title="Content">🖋</a> <a href="#ideas-rneher" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center"><a href="https://github.com/trvrb"><img src="https://avatars.githubusercontent.com/u/1176109?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Trevor Bedford</b></sub></a><br /><a href="#ideas-trvrb" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center"><a href="https://twitter.com/hamesjadfield"><img src="https://avatars1.githubusercontent.com/u/8350992?v=4?s=75" width="75px;" alt=""/><br /><sub><b>james hadfield</b></sub></a><br /><a href="https://github.com/hodcroftlab/covariants/commits?author=jameshadfield" title="Code">💻</a> <a href="#design-jameshadfield" title="Design">🎨</a> <a href="https://github.com/hodcroftlab/covariants/commits?author=jameshadfield" title="Documentation">📖</a> <a href="#ideas-jameshadfield" title="Ideas, Planning, & Feedback">🤔</a></td> <td align="center"><a href="https://github.com/MoiraZuber"><img src="https://avatars1.githubusercontent.com/u/48066606?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Moira Zuber</b></sub></a><br /><a href="https://github.com/hodcroftlab/covariants/commits?author=MoiraZuber" title="Code">💻</a> <a href="#data-MoiraZuber" title="Data">🔣</a></td> <td align="center"><a href="http://jamesscottbrown.com/"><img src="https://avatars.githubusercontent.com/u/338833?v=4?s=75" width="75px;" alt=""/><br /><sub><b>James Scott-Brown</b></sub></a><br /><a href="#ideas-jamesscottbrown" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/hodcroftlab/covariants/commits?author=jamesscottbrown" title="Code">💻</a> <a href="#design-jamesscottbrown" title="Design">🎨</a></td> </tr> <tr> <td align="center"><a href="http://theo.io/"><img src="https://avatars2.githubusercontent.com/u/19732295?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Theo Sanderson</b></sub></a><br /><a href="#content-theosanderson" title="Content">🖋</a> <a href="https://github.com/hodcroftlab/covariants/commits?author=theosanderson" title="Code">💻</a> <a href="https://github.com/hodcroftlab/covariants/commits?author=theosanderson" title="Documentation">📖</a></td> <td align="center"><a href="https://github.com/babarlelephant"><img src="https://avatars.githubusercontent.com/u/6537565?v=4?s=75" width="75px;" alt=""/><br /><sub><b>babarlelephant</b></sub></a><br /><a href="#content-babarlelephant" title="Content">🖋</a></td> <td align="center"><a href="https://research.fhcrc.org/bloom/en.html"><img src="https://avatars1.githubusercontent.com/u/1906801?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Jesse Bloom</b></sub></a><br /><a href="#content-jbloom" title="Content">🖋</a></td> <td align="center"><a href="https://github.com/corneliusroemer"><img src="https://avatars1.githubusercontent.com/u/25161793?v=4?s=75" width="75px;" alt=""/><br /><sub><b>Cornelius Roemer</b></sub></a><br /><a href="#content-corneliusroemer" title="Content">🖋</a></td> <td align="center"><a href="https://github.com/acx01b"><img src="https://avatars.githubusercontent.com/u/6537565?v=4?s=75" width="75px;" alt=""/><br /><sub><b>acx01b</b></sub></a><br /><a href="#content-acx01b" title="Content">🖋</a></td> <td align="center"><a href="https://github.com/rasenschachmatt"><img src="https://avatars.githubusercontent.com/u/19908919?v=4?s=75" width="75px;" alt=""/><br /><sub><b>rasenschachmatt</b></sub></a><br /><a href="#content-rasenschachmatt"