Using Nanopore Technology for Real Time, Direct, Scalable DNA/RNA Sequencing

Overview

Course Overview

The goal of this course is to teach the fundamentals of nanopore sequencing using the Oxford Nanopore Technologies (ONT) platform. We will start with an introduction into ONT technology and devices, with the goal of covering end to end the workflow for preparation and analysis of bacterial samples using examples of a whole genome approach and a targeted barcoded amplicon approach. This course will cover the wet lab preparation of libraries from genomic DNA, with a focus on the critical steps and potential pitfalls and understanding what constitutes a ‘good’ sample for purpose of best results using the technology. Also, training includes how to use MinKNOW GUI for GridION and MinION devices and a discussion of the methods available for basecalling and analysis of samples for species identification, including use of opens source tools for mapping and assembly, such as Minimap2 and Canu.

Audience

This course is directed towards molecular biologists, bioinformaticians, scientists and technicians who want to apply Oxford Nanopore Sequencing technology in their labs. Knowledge of ONT sequencing technology is desirable but not essential. Practical experience with standard molecular biology techniques required. 

Modules/Resources

Introduction to ONT devices and latest technology
Wet lab training and best practices for sample quality and library preparation for Nanopore sequencing
Running MinKNOW and real-time sequencing data handling
Introduction to basecalling and analysis tools (ONT and opens source) for analysis of ONT data

Learning Outcomes

After this course you should be able to:
-Prepare libraries from genomic DNA for amplicon or whole genome approaches to nanopore sequencing
-Run ONT devices and assess sequencing performance during a run
-Understand the basics of ONT data handling and analysis
-Analyse and interpret ONT amplicon data and whole genomic data from bacterial samples

Speakers

Speakers, Trainers and Organisers

Margherita Coccia

Oxford Nanopore Technologies Ltd

UK

Michael Micorescu

Oxford Nanopore Technologies, Ltd

UK

Stephen Rudd

Oxford Nanopore Technologies, Ltd

UK

Scientific Organisers

Vladimir Benes

EMBL Heidelberg

Germany

Margherita Coccia

Oxford Nanopore Technologies Ltd

UK

Course Organisers

Maryann Heck

EMBL Heidelberg

Germany

Programme