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Introduction to Oxford Nanopore Technology data analyses

The South Green/i-trop Platform organizes a 5-days course at CERAAS (Thies, Senegal) from November 8 to 12, 2021. The goal of this course is to introduce nanopore sequencing using Oxford Nanopore Technologies (ONT).
It included a web lab training for library preparation and bioinformatics training for analysis of ONT data. It specially focused on the following aspects : basecalling, reads quality control, assemblies and polishing/correction, contig quality and structural variants detection.
This course is directed towards molecular biologists and scientists who want to apply Oxford Nanopore Sequencing technology in their labs based in West Africa.


Linux and knowledge of NGS formats


  • Introduction to the principles of the technology (kits, flowcell)
  • Principles of basecalling
  • Handling mapping and assembly tools suitable for ONT data
  • How to polish and correct an assembly
  • Detecting structural variations with long reads

Learning objectives

  • Understanding limits and advantages of ONT technology
  • Manipulating ONT data on a virtual machine on jupyter environment
  • Handling mapping, assembly, polishing tools and be able to analyse your own data
  • Detecting structural variations using long reads

Training material

Organizers and Instructors

Marie Couderc, Philippe Cubry, Cédric Mariac, Julie Orjuela, François Sabot, Julien Serret et Christine Tranchant