ncov-recombinant

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ncov-recombinant

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Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

ncov-recombinant 최신버젼 다운로드

최종 버전 다운로드 (.zip)

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# ncov-recombinant

> ❗❗❗ 
> **Note**: ncov-recombinant will be deprecated soon as SARS-CoV-2 recombination has evolved beyond the scope of this pipeline's design. The new tool will be [rebar](https://github.com/phac-nml/rebar), which is under active development. 
> ❗❗❗

[![All Contributors](https://img.shields.io/badge/all_contributors-10-orange.svg?style=flat-square)](https://raw.githubusercontent.com/ktmeaton/ncov-recombinant/master/)

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/ktmeaton/ncov-recombinant/blob/master/LICENSE)
[![GitHub issues](https://img.shields.io/github/issues/ktmeaton/ncov-recombinant.svg)](https://github.com/ktmeaton/ncov-recombinant/issues)
[![Install CI](https://github.com/ktmeaton/ncov-recombinant/actions/workflows/install.yaml/badge.svg)](https://github.com/ktmeaton/ncov-recombinant/actions/workflows/install.yaml)
[![Pipeline CI](https://github.com/ktmeaton/ncov-recombinant/actions/workflows/pipeline.yaml/badge.svg)](https://github.com/ktmeaton/ncov-recombinant/actions/workflows/pipeline.yaml)

Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

1. Align sequences and perform clade/lineage assignments with [Nextclade](https://github.com/nextstrain/nextclade).
1. Identify parental clades and plot recombination breakpoints with [sc2rf](https://github.com/lenaschimmel/sc2rf).
1. Create tables, plots, and powerpoint slides for reporting.

Please refer to the [**documentation**](https://ncov-recombinant.readthedocs.io/en/stable/) for detailed instructions on installing, running, developing and much more!

## Credits

[ncov-recombinant](https://github.com/ktmeaton/ncov-recombinant) is built and maintained by [Katherine Eaton](https://ktmeaton.github.io/) at the [National Microbiology Laboratory (NML)](https://github.com/phac-nml) of the Public Health Agency of Canada (PHAC).

<table>
 <tr>
 <td align="center"><a href="https://ktmeaton.github.io"><img src="https://s.gravatar.com/avatar/0b9dc28b3e64b59f5ce01e809d214a4e?s=80" width="100px;" alt=""/> Katherine Eaton</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=ktmeaton" title="Code">💻</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=ktmeaton" title="Documentation">📖</a> <a href="#design-ktmeaton" title="Design">🎨</a> <a href="#ideas-ktmeaton" title="Ideas, Planning, & Feedback">🤔</a> <a href="#infra-ktmeaton" title="Infrastructure (Hosting, Build-Tools, etc)">🚇</a> <a href="#maintenance-ktmeaton" title="Maintenance">🚧</a></td>
 </tr>
</table>

Thanks goes to these wonderful people ([emoji key](https://allcontributors.org/docs/en/emoji-key)):

<table>
 <tr>
 <td align="center"><a href="https://github.com/nextstrain/nextclade"><img src="https://avatars.githubusercontent.com/u/22159334?v=4?s=100" width="100px;" alt=""/> Nextstrain (Nextclade)</a> <a href="#data-nextstrain" title="Data">🔣</a> <a href="#plugin-nextstrain" title="Plugin/utility libraries">🔌</a></td>
 <td align="center"><a href="https://github.com/lenaschimmel/sc2rf"><img src="https://avatars.githubusercontent.com/u/1325019?v=4?s=100" width="100px;" alt=""/> Lena Schimmel (sc2rf)</a> <a href="#plugin-lenaschimmel" title="Plugin/utility libraries">🔌</a></td>
 <td align="center"><a href="https://github.com/yatisht/usher"><img src="https://avatars.githubusercontent.com/u/34664884?v=4?s=100" width="100px;" alt=""/> Yatish Turakhia (UShER)</a> <a href="#data-yatisht" title="Data">🔣</a> <a href="#plugin-yatisht" title="Plugin/utility libraries">🔌</a></td>
 <td align="center"><a href="https://github.com/yatisht/usher"><img src="https://avatars.githubusercontent.com/u/186983?v=4?s=100" width="100px;" alt=""/> Angie Hinrichs (UShER)</a> <a href="#data-AngieHinrichs" title="Data">🔣</a> <a href="#plugin-AngieHinrichs" title="Plugin/utility libraries">🔌</a></td>
 <td align="center"><a href="https://www.inspq.qc.ca/en/auteurs/2629/all"><img src="https://i1.rgstatic.net/ii/profile.image/278724097396748-1443464411327_Q128/Benjamin-Delisle.jpg?s=100" width="100px;" alt=""/> Benjamin Delisle</a> <a href="https://github.com/ktmeaton/ncov-recombinant/issues?q=author%3Abenjamindeslisle" title="Bug reports">🐛</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=benjamindeslisle" title="Tests">⚠️</a></td>
 </tr>
 <tr>
 <td align="center"><a href="https://ca.linkedin.com/in/dr-vani-priyadarsini-ikkurti-4a2ab676"><img src="https://media-exp1.licdn.com/dms/image/C5603AQHaG8Xx4QLXSQ/profile-displayphoto-shrink_200_200/0/1569339145568?e=2147483647&v=beta&t=3WrvCciW-x8J3Aw4JHGrWOpuqiikrrGV2KsDaISnHIw" width="100px;" alt=""/> Vani Priyadarsini Ikkurthi</a> <a href="https://github.com/ktmeaton/ncov-recombinant/issues?q=author%3Avanipriyadarsiniikkurthi" title="Bug reports">🐛</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=vanipriyadarsiniikkurthi" title="Tests">⚠️</a></td>
 <td align="center"><a href="https://ca.linkedin.com/in/mark-horsman-52a14740"><img src="https://ui-avatars.com/api/?name=Mark+Horsman?s=100" width="100px;" alt=""/> Mark Horsman</a> <a href="#ideas-markhorsman" title="Ideas, Planning, & Feedback">🤔</a> <a href="#design-markhorsman" title="Design">🎨</a></td>
 <td align="center"><a href="https://github.com/jbloomlab"><img src="https://avatars.githubusercontent.com/u/17679492?s=200&v=4?s=100" width="100px;" alt=""/> Jesse Bloom Lab</a> <a href="#data-jbloomlab" title="Data">🔣</a> <a href="#plugin-jbloomlab" title="Plugin/utility libraries">🔌</a></td>
 <td align="center"><a href="https://github.com/dfornika"><img src="https://avatars.githubusercontent.com/u/145659?v=4?s=100" width="100px;" alt=""/> Dan Fornika</a> <a href="#ideas-dfornika" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=dfornika" title="Tests">⚠️</a></td>
 <td align="center"><img src="https://ui-avatars.com/api/?name=Tara+Newman?s=100" width="100px;" alt=""/> Tara Newman <a href="#ideas-TaraNewman" title="Ideas, Planning, & Feedback">🤔</a> <a href="https://github.com/ktmeaton/ncov-recombinant/commits?author=TaraNewman" title="Tests">⚠️</a></td>
 </tr>
</table>

This project follows the [all-contributors](https://github.com/all-contributors/all-contributors) specification. Contributions of any kind welcome!

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