View Code? Open in Web Editor NEW

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

License: MIT License

Shell 4.22% JavaScript 2.00% Python 3.88% Perl 0.27% Rust 41.91% TypeScript 44.17% TeX 0.58% Makefile 0.16% Jupyter Notebook 0.48% Dockerfile 1.02% SCSS 0.90% MDX 0.40%

nextclade's Introduction

Nextclade

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

by Nextstrain team

🌎 clades.nextstrain.org

📜️ 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} 🤔 ⚠️ 📢 👀	_{Thomas Sibley} 🚇 🛡️	_{Victor Lin} 💻 📖	_{Theo Sanderson} 💻	_{Natalie Stroud} 🖋 🌍	_{Alex Rubinsteyn} 📖	_{Christopher Bottoms} 📖	_{Finlay Maguire} 📖
_dnanto 💻 🔣