ncov2019-artic-nf

Bioinformatics workflow

Automates bioinformatics analysis of SARS-COV2 sequencing data using the ARTIC network's fieldbioinformatics tools.

A Nextflow pipeline for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics), with a focus on ncov2019

GitHub

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Language: Nextflow
last commit: almost 3 years ago
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