Nextclade

Viral genome clade assignment, mutation calling, and sequence quality checks

by Nextstrain team

🌎 clades.nextstrain.org

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📜️ Citation

If you use results obtained with Nextclade in a publication, please

• cite our paper:

  Aksamentov, I., Roemer, C., Hodcroft, E. B., & Neher, R. A., (2021). Nextclade: clade assignment, mutation calling and quality control for viral genomes. Journal of Open Source Software, 6(67), 3773, https://doi.org/10.21105/joss.03773

  (bibtex)

• where possible, provide a link to Nextclade Web:

  https://clades.nextstrain.org

📗 Documentation

• Documentation for Nextclade: https://docs.nextstrain.org/projects/nextclade
• Documentation for the parent project, Nextstrain: https://docs.nextstrain.org

🧑‍💻 Development

If you are a developer, curious about how Nextclade and Nextalign work, want to modify it or contribute new features or fixes, check out out developer's guides:

• "Developer's guide: Nextclade CLI and Nextalign CLI"

• "Developer's guide: Nextclade Web"

📦 Packages

This repository consists of a set of packages presented in the table below. Refer to README files of individual packages for more details.

Package	Type	Get	Docker images
nextalign	C++ library
nextalign_cli	C++ executable	📥 Github Releases	🐋 nextstrain/nextalign
nextclade	C++ library
nextclade_cli	C++ executable	📥 Github Releases	🐋 nextstrain/nextclade
nextclade_wasm	WebAssembly module
nextclade_web	Web App	🌎 clades.nextstrain.org

✨ Team

Nextclade is a part of Nextstrain project .

It is maintained by:

Ivan Aksamentov Senior Software Engineer NeherLab, Biozentrum, University of Basel Swiss Institute of Bioinformatics

Richard Neher Principal Investigator NeherLab, Biozentrum, University of Basel Swiss Institute of Bioinformatics

Cornelius Roemer Staff Scientist NeherLab, Biozentrum, University of Basel Swiss Institute of Bioinformatics

We are thankful to all our contributors, no matter how they contribute: in ideas, science, code, documentation or otherwise. Thanks goes to these people (emoji key):

Emma Hodcroft 🤔 ⚠️ 📢 👀	Thomas Sibley 🚇 🛡️	Victor Lin 💻 📖	Theo Sanderson 💻	Natalie Stroud 🖋 🌍	Alex Rubinsteyn 📖	Christopher Bottoms 📖	Finlay Maguire 📖
dnanto 💻 🔣

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

🏢 Sponsors

We are thankful to the following companies who supported us:

Vercel for sponsoring Nextclade builds on their platform

⚖️ License

MIT License