CoV-Spectrum

CoV-Spectrum is an interactive tool to analyze and discover variants of SARS-CoV-2. Details about the features and purpose of CoV-Spectrum can be found on the About page. Feature proposals, bug reports and other suggestions for improvements are very welcome. Please submit them through the Issues function of this repository.

Contributors ✨

Thanks goes to these wonderful people (emoji key):

Chaoran Chen 💻 🔣 🤔 🚧 📦 🔬 🚇	tanja819 🤔	Sarah Nadeau 🤔 🔣 💻	Michael Yared 💻	Philippe Voinov 💻	ningxie 💻	Cornelius Roemer 🤔
DrYak 🔣	gautier-collab 💻	David Meyer 💻	Anastasia Escher 💻	Theo Sanderson 💻 🤔	Adrian Lison 💻	Fabian Engelniederhammer 💻
Jonas Kellerer 💻	Philip Schulz 💻	Taepper 💻 🤔 🔬	GeorgKreuzmayr 💻 🔬	Daniel Grittner 💻 🔬

This project follows the all-contributors specification. Contributions of any kind welcome!

Developer documentation

From a technical point of view, CoV-Spectrum's frontend is a React app that shows a lot of plots based on read-only data. It depends on the CoV-Spectrum server for all but sequence data and on LAPIS for the sequence data. Please check out the corresponding repositories for instructions on how to set up the server applications. A short guide on how to get the frontend application running locally is in ./docs/building.md.

There is documentation about different technical aspects of this app in the ./docs folder. These next few paragraphs link to parts of that documentation. If you don't want to read much doc, at least check the the list of gotchas (./docs/gotchas.md).

There is a loose logic to how the source code folder is structured. See ./docs/folders.md for a guide.

No state management library (e.g. Redux) is used. Most data is in a generic format which is loaded centrally and transformed per plot. Some more specialized data is loaded locally in components. In either case, data is fetched through API helper functions (./docs/api.md).

The plotting libraries that we use are Recharts and Plotly. See ./docs/plot-libraries.md for a bit more info.

There is a special setup that allows certain plots to be loaded standalone outside of the main app (embedded in IFrames). This widget system requires special care when passing props and loading data. It is documented in ./docs/widgets.md.

Certain models and analyses require very different data than the main application. They are slightly separated from the rest of the code. See ./docs/models.md.

There is also some miscellaneous documentation about date handling (./docs/date-cache.md), routing (./docs/routing.md), export buttons (./docs/export.md) and styling (./docs/styling.md).

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