Nextclade

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

by Nextstrain team

🌎 clades.nextstrain.org

nextclade.mp4
Brief demonstration of Nextclade Web. Large version is here.

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📥 Installation and usage

🌍 Web	clades.nextstrain.org	guide
📥 CLI	Linux x86_64 glibc musl* Linux ARM64 glibc musl* macOS*** Apple Silicon Intel Windows x86_64 .exe	install usage all releases
🐋 Docker	docker pull nextstrain/nextclade:latest (tags)	guide
🐍 Conda	conda install -c bioconda nextclade (versions)**	guide
🛠️ From source	github.com/nextstrain/nextclade	guide
💾 Datasets	github.com/nextstrain/nextclade_data	guide
📚 Docs	docs.nextstrain.org/projects/nextclade
🚩 Issues	Report bugs, suggest features
💬 Discussion	discussion.nextstrain.org

_{* glibc builds are faster and recommended, but require glibc >= 2.14. musl builds are static, run on older Linux distributions, and are slightly slower
** Bioconda releases need manual approval and can be delayed
*** macOS executables are not signed. See the install guide if macOS refuses to run them}

📜️ 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

Read developer guide here: docs/dev/developer-guide.md

✨ 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 🤔 ⚠️ 📢 👀	Anna Parker 💻 ⚠️ 🤔	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!

⚖️ License

MIT License