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boydgreenfield authored Mar 31, 2020
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SARS-CoV-2 variant calling and consensus assembly pipeline using [ivar](https://github.com/andersen-lab/ivar) and [minimap2](https://github.com/lh3/minimap2).

⚠️ **As of March 24th, this pipeline support ARTIC v1 primers, capture-based approaches, and RNA-seq _on Illumina platforms_. We expect to add ONT support in the coming days, but recommend looking at the [ARTIC Network protocol](https://artic.network/ncov-2019) in the meantime.**
⚠️ **As of April 1st, this pipeline support ARTIC v1 primers, capture-based approaches, and RNA-seq _on Illumina platforms_. We expect to add ONT support in the coming days, but recommend looking at the [ARTIC Network protocol](https://artic.network/ncov-2019) in the meantime.**

# Quick start

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