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

License: MIT License

JavaScript 1.75% TypeScript 36.07% Python 9.90% Dockerfile 0.41% Shell 5.30% SCSS 1.15% CMake 2.85% Makefile 0.29% C++ 40.83% C 1.31% Batchfile 0.06% PowerShell 0.06% Ruby 0.01%

nextclade's Introduction

Nextclade

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

by Nextstrain team

🌎 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:

📦 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

Richard Neher

Principal Investigator
NeherLab, Biozentrum, University of Basel

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):