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https://github.com/nextstrain/nextclade

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
https://github.com/nextstrain/nextclade

clade clades coronavirus covid covid-19 covid19 dna influenza ncov neherlab next-generation-sequencing nextstrain research rna sars-cov-2 science sequences sequencing strain virus

Last synced: 3 months ago
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Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

Host: GitHub
URL: https://github.com/nextstrain/nextclade
Owner: nextstrain
License: mit
Created: 2020-06-12T13:01:14.000Z (over 4 years ago)
Default Branch: master
Last Pushed: 2024-07-17T13:31:43.000Z (4 months ago)
Last Synced: 2024-07-17T16:37:40.501Z (4 months ago)
Topics: clade, clades, coronavirus, covid, covid-19, covid19, dna, influenza, ncov, neherlab, next-generation-sequencing, nextstrain, research, rna, sars-cov-2, science, sequences, sequencing, strain, virus
Language: Rust
Homepage: https://clades.nextstrain.org
Size: 59.2 MB
Stars: 204
Watchers: 20
Forks: 58
Open Issues: 115
Metadata Files:
- Readme: README.md
- Changelog: CHANGELOG.md
- Contributing: CONTRIBUTING.md
- License: LICENSE

Awesome Lists containing this project

README

Nextclade

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

by Nextstrain team

🌎 clades.nextstrain.org

| |
|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| Brief demonstration of Nextclade Web. Large version is here. |

---

📜️ 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](https://clades.nextstrain.org/citation.bib))

- 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](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
💻 🔣