Location & dates EMBL Heidelberg, Germany 12 - 15 Jun 2018
Deadlines Application closed

EMBL Courses and Conferences during the Coronavirus pandemic

With the onsite programme paused, many of our events are now being offered in virtual formats.

Registration is open as usual for many events, with back-up plans in place to move further courses and conferences online as necessary. Registration fees for any events affected by the COVID-19 disruption are fully refundable.

More information for participants of events at EMBL Heidelberg can be found here.

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.


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. 


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

This course is kindly supported by the EMBL Genomics Core Facility.


EMBL Courses and Conferences are kindly supported by our Corporate Partnership Programme

Founder partners

  • Leica logo
  • Olympus logo

Corporate partners

  • 10x Genomics_120x82
  • Becton Dickinson logo
  • Bio-Rad logo
  • Boehringer Ingelheim logo
  • Eppendorf logo
  • GSK logo
  • Milteniy Biotec logo
  • NetApp logo
  • Stilla logo
  • ThermoFisher logo

Associate partners

  • Merck logo
  • New England Biolabs logo
  • Nikon logo
  • Promega logo
  • Roche logo
  • Sanofi logo
  • Sartorius logo