Nextclade

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

by Nextstrain team

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

📥 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 💻 🔣