nokcs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting

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.

Introduction

The wf-artic workflow implements a slightly modified ARTIC FieldBioinformatics workflow for the purpose of preparing consensus sequences from SARS-CoV-2 genomes that have been DNA sequenced using a pooled tiling amplicon strategy.

The workflow consumes a folder containing demultiplexed sequence reads as prepared by either MinKNOW or Guppy. The workflow needs to know the primer scheme that has been used during genome amplication and library preparation e.g. ARTIC/V3 or ONT_Midnight/V1. Other parameters can be specified to e.g. assign sample names to the barcodes or to adjust the length distribution of acceptable amplicon sequences.

DNA sequences in FASTQ format are aggregated, filtered for sequence length and quality characteristics and are mapped to the reference SARS-CoV-2 genome using minimap2. A primer-scheme specific bed file is used to identify the regions of the mapped sequences that correspond to synthetic sequences (primers) - these regions are clipped to ensure that sequences are entirely of biological origin. The retained sequences are used to prepare a consensus sequence that is then polished using Medaka and variant calling is performed to produce a VCF file of genetic differences relative to the reference genome. The consensus sequence is annotated for virus clade information using NextClade and a strain assignment is performed using Pangolin.

The completed analysis is summarised in an HTML format report that summarises key information that includes number of reads, depth of coverage information per amplicon and both the Nextclade and Pangolin information.

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