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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, which is under active development.
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Reproducible workflow for SARS-CoV-2 recombinant sequence detection.

1. Align sequences and perform clade/lineage assignments with Nextclade.
2. Identify parental clades and plot recombination breakpoints with sc2rf.
3. Create tables, plots, and powerpoint slides for reporting.

Please refer to the documentation for detailed instructions on installing, running, developing and much more!

ncov-recombinant is built and maintained by Katherine Eaton at the National Microbiology Laboratory (NML) of the Public Health Agency of Canada (PHAC).

Katherine Eaton 💻 📖 🎨 🤔 🚇 🚧

Thanks goes to these wonderful people (emoji key):

Nextstrain (Nextclade) 🔣 🔌	Lena Schimmel (sc2rf) 🔌	Yatish Turakhia (UShER) 🔣 🔌	Angie Hinrichs (UShER) 🔣 🔌	Benjamin Delisle 🐛 ⚠️
Vani Priyadarsini Ikkurthi 🐛 ⚠️	Mark Horsman 🤔 🎨	Jesse Bloom Lab 🔣 🔌	Dan Fornika 🤔 ⚠️	Tara Newman 🤔 ⚠️

This project follows the all-contributors specification. Contributions of any kind welcome!