South Green Logo

South Green Trainings pages

Introduction to Oxford Nanopore Technology data analyses

This course offers an introduction to ONT data analysis. It includes 5 issues: basecalling, reads quality control, assemblies and polishing/correction, contig quality and structural variants detection.


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


  • Julie Orjuela (JO) -
  • Francois Sabot (FS) -
  • Gautier Sarah (GS) -
  • Sébastien Ravel (SR) -


Date Location Topics Participants Instructors Links Units
2023 Montpellier, France Introduction to ONT data analyses 12 JO, FS, GS, SR   UMR DIADE, AGAP, PHIM
2021 Zoom from Montpellier, France Introduction to ONT data analyses 14 JO, FS, GS   UMR DIADE, AGAP