wf-artic documentation
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 amplification and library preparation
e.g. ARTIC/V3 or ONT_Midnight/V1. Other parameters can be specified too e.g.
assign sample names to the barcodes or to adjust the length distribution of
acceptable amplicon sequences. The Medaka variant model is selected based on the
provided basecaller configuration (using the parameter --basecaller_cfg), or
alternatively the Medaka model can be provided directly via the --medaka_variant_model
parameter.
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.
More information can be found in these two blog posts:
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 Singularity to provide isolation of the required software. Both methods are automated out-of-the-box provided either Docker or Singularity 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 our 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.
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