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Nanopore Learning / Courses /
Nanopore sequencing the SARS-CoV-2 genome

This course brings together new and existing content to guide you through genomic sequencing of SARS-CoV-2 using the ARTIC workflow and nanopore sequencing and analysis.

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Course overview

Introduction

1 SARS-CoV-2: Course Introduction
2 Introduction to Oxford Nanopore Technologies - The Company
3 Introduction: Nanopore sequencing

Preparing your Sample

4 SARS-CoV-2: The ARTIC protocol and how it works
5 SARS-CoV-2: Options for whole genome sequencing protocols
6 SARS-CoV-2: Classic ARTIC protocol
7 SARS-CoV-2: Eco ARTIC protocol
8 SARS-CoV-2: Midnight Protocol

Sequencing

9 MinKNOW: Introduction
10 MinKNOW: Installation
11 MinKNOW: Hardware check
12 MinKNOW: Flow cell check
13 MinION Mk1C unboxing and configuring
14 A practical demonstration of priming and loading a flow cell
15 SARS-CoV-2: Setting up a new ARTIC experiment
16 MinKNOW: Assessing your run

Analysis

17 SARS-CoV-2: ARTIC analysis workflow overview
18 SARS-CoV-2: ARTIC workflow data and analysis files
19 SARS-CoV-2: ARTIC Field Bioinformatics analysis technical details
20 Data Analysis: EPI2ME Labs introduction
21 SARS-CoV-2: EPI2ME Labs ARTIC analysis demonstration
22 SARS-CoV-2: Secondary analysis post ARTIC analysis

SARS-CoV-2: Eco ARTIC protocol

19 min
Learning objectives
  • To understand the different steps of the protocol and importance of each steps.
  • importance of batching samples of differing ct values to prevent drop out of samples with low viral counts.
  • The need for controls
  • Good laboratory practice to prevent contamination
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