artic-mn is a nextflow workflow for analysis of SARS-CoV-2 sequencing data generated on Oxford Nanopore sequencers using libraries created with protocols based on the ARTIC SARS-CoV-2 sequencing protocol.
This workflow started as a streamlined version of the monroe ont_assembly workflow created for the StaPH-B Toolkit by Kelsey Florek, Abigail Shockey, and others. Considerable flexibility and functionality has been removed to adapt the workflow to the needs of our lab. If you are here because you need a COVID sequencing workflow consider using any one of the many workflows built into the StaPH-B Toolkit.