Advanced Training with Oxford Nanopore Technologies

Overview

Course overview 

The goal of this course is to teach 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 workflows for the preparation and analysis of human and yeast samples using whole genome and barcoded cDNA sequencing approaches. This course will cover the wet lab preparation of libraries from genomic DNA and total RNA, 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. The training includes an overview of the MinKNOW GUI for GridION and MinION devices. We then cover methods available for basecalling and analysis of samples for structural variants and differential gene expression, using both Oxford Nanopore and open source tools. 

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. 

Modules/Resources 

During this course we will focus on the following aspects: 

• 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 human genomic DNA for nanopore sequencing 
• Prepare libraries from total yeast RNA for nanopore sequencing 
• Run ONT devices and assess sequencing performance during a run 
• Understand the basics of ONT data handling and analysis 
• Analyze and interpret ONT whole genome data for structural variant detection 
• Analyze and interpret ONT RNA data for differential gene expression profiling 

This course is co-organised with Oxford Nanopore Technologies.

Speakers

Speakers and Trainers

Bianka Baying

EMBL Heidelberg

Germany

Aaron Brooks

EMBL Heidelberg

Germany

Christoph Dieterich

Heidelberg University Hospital

Germany

Dinko Pavlinic

EMBL Heidelberg

Germany

Manuela Saathoff

Oxford Nanopore Technologies

UK

Scientific Organisers

Vladimir Benes

EMBL Heidelberg

Germany

Margherita Coccia

Oxford Nanopore Technologies

UK

Michael Micorescu

Oxford Nanopore Technologies

UK

Course Organisers

Christina Dollt

EMBL Heidelberg

Germany

Programme