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Nanopore sequencing the SARS-CoV-2 genome - webinars

Tue 7th April - Thu 9th April 2020

Online

Oxford Nanopore's sequencing technology has been used to sequence the Sars-CoV-2 virus in 7 hours.  Many researchers are using the portable MinION device, with higher throughput labs using the larger GridION, and initial work starting on the ultra-high throughput PromethION.  Early work on the smallest Flongle is expected to emerge soon.

Oxford Nanopore scientists will present two webinars, giving you an introduction to sequencing the virus using their protocol and an introduction to the software solutions available for analysis.

Please note that each webinar will be run twice (at different times, on different days).

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

 

Nanopore sequencing the SARS-CoV-2 genome: introduction to protocol

Webinar 1: 4:00 pm (BST), Tuesday 7th April 2020  
Webinar 2: 9:00 am (BST), Wednesday 8th April 2020

During this online seminar, Oxford Nanopore will provide an in-depth introduction to sequencing the SARS-CoV-2 genome using their protocol including advice for best performance.

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. 

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