Event:

Bioinformatics workflows for SARS-CoV-2; from raw Nanopore reads to consensus genomes using the ARTIC coronavirus protocol

Webinar 1: 4:00 pm (BST), Wednesday 8th April 2020
Webinar 2: 9:00 am (BST), Thursday 9th April 2020

The ARTIC network has published a bioinformatics protocol for the analysis of Nanopore sequenced SARS-CoV-2 genomes.

In this session we will first explore how the Rampart software can be used to track the performance of a sequence run. The ARTIC FieldBioinformatics protocol will be followed to prepare a consensus sequence and lists of SNPs from publicly available sequence SARS-CoV-2 sequence collections. Stephen Rudd will introduce two Docker containers that have packaged the ARTIC software and will demonstrate how these containers can be used to streamline a Nanopore-based sequence analysis workflow.

Participation in this knowledge exchange should:

  1. Provide an introduction to the ARTIC software solutions for SARS-CoV-2 genome analysis and an understanding of when Rampart and FieldBioinformatics software should be used
  2. Facilitate independent analysis of SARS-CoV-2 FASTQ files using containerised ARTIC workflows. 


Following the presentation, Oxford Nanopore team members will be available to answer questions live.
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