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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.

Prerequisites

Linux and knowledge of NGS formats

Program

  • 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

Instructors

  • Julie Orjuela (JO) - julie.orjuela@ird.fr
  • Francois Sabot (FS) - francois.sabot@ird.fr
  • Gautier Sarah (GS) - gautier.sarah@inrae.fr

Trainings

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