Streamline SARS-CoV-2 Analysis: A Guide to the ARTIC Workflow for Rapid Genome Sequencing

Are you looking for a streamlined way to analyze SARS-CoV-2 genomic data? The ARTIC SARS-CoV-2 workflow offers a robust solution for preparing consensus sequences from tiled amplicon sequencing data. This comprehensive guide walks you through the key features, benefits, and steps to implement this powerful workflow.

What is the ARTIC SARS-CoV-2 Workflow?

The ARTIC SARS-CoV-2 workflow is a bioinformatics pipeline designed to process sequencing data generated using the ARTIC network's amplicon-based sequencing protocol. It's specifically tailored for Oxford Nanopore Technologies (ONT) data, enabling researchers and public health professionals to rapidly generate consensus sequences, identify variants, and perform lineage assignment for SARS-CoV-2 samples. This allows for faster monitoring and tracking of viral evolution.

Key Benefits of the ARTIC Workflow

• Rapid analysis: Get results in approximately 5 minutes per sample and accelerate your research.
• Simplified implementation: Leverage Docker or Singularity containers for easy setup and execution.
• Standardized methodology: Implement a slightly modified ARTIC FieldBioinformatics workflow for consistent results.
• Comprehensive reporting: Generate detailed reports with coverage metrics, variant summaries, and lineage assignments.

System Requirements

Before diving in, ensure your system meets these recommendations:

• Recommended: 4 CPUs, 8 GB Memory
• Minimum: 2 CPUs, 4 GB Memory
• ARM processor support: No

Step-by-Step Installation and Execution

1. Install Nextflow: This workflow uses Nextflow to manage software resources. If you don't have it installed, get it from https://www.nextflow.io/.

2. Obtain the Workflow: Use the following command to download the workflow and view available parameters:

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

3. Download Demo Data: Test the workflow using the provided demo dataset:

   wget https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/wf-artic/wf-artic-demo.tar.gz
   tar -xzvf wf-artic-demo.tar.gz
   

4. Run the Workflow: Execute the workflow with the demo data:

   nextflow run epi2me-labs/wf-artic \
   --fastq test_data/reads.fastq.gz \
   -profile standard
   

Input Options: Tailoring the Workflow to Your Data

• FASTQ Files: Accepts single FASTQ files, directories of FASTQ files, or directories containing multiplexed FASTQ files in sub-directories.
• Sample Sheets: Use a CSV file to map barcodes to sample aliases when analyzing multiplexed data.
• Primer Scheme Selection: Specify the primer scheme used during library preparation (e.g., ARTIC/V3, ONT_Midnight/V1).

Output Options: Understanding Your Results

The workflow generates a variety of output files including:

• Workflow report: An HTML report summarizing the analysis for all samples.
• Consensus sequences: A FASTA file containing the final consensus sequences for each sample.
• Pangolin results: CSV file detailing lineage assignments for each sample, aiding in tracking the spread and evolution of SARS-CoV-2 variants.
• Nextclade results: JSON file including information about the genetic clades each sample belongs to.
• Variants: VCF files containing high-confidence variants identified in each sample, facilitating deeper analysis of viral mutations.

Optimize Your SARS-CoV-2 Analysis Today

The ARTIC SARS-CoV-2 workflow offers a powerful and efficient solution for analyzing viral sequencing data. By following this guide, you can quickly implement the workflow and begin generating valuable insights into the evolution and spread of SARS-CoV-2. Simplify your workflow, improve your turnaround time.