ARTIC SARS-CoV-2 Workflow

This repository contains a nextflow workflow for running the ARTIC SARS-CoV-2 workflow on multiplexed MinION, GridION, and PromethION runs.

Quickstart

The workflow uses nextflow to manage compute and software resources, as such nextflow will need to be installed before attempting to run the workflow.

The workflow can currently be run using either Docker or conda to provide isolation of the required software. Both methods are automated out-of-the-box provided either docker of conda is installed.

It is not required to clone or download the git repository in order to run the workflow. For more information on running EPI2ME Labs workflows visit out website.

Workflow options

To obtain the workflow, having installed nextflow, users can run:

nextflow run epi2me-labs/wf-artic --help

to see the options for the workflow.

Workflow outputs

The primary outputs of the workflow include:

• a FASTA file containing the consensus sequence for all samples,
• a VCF file sample all samples,
• an HTML report document detailing QC metrics and the primary findings of the workflow.

Useful links

• medaka
• artic
• nextflow
• docker
• conda