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Introduction to Oxford Nanopore Technology data analyses for metaviromics

This course offers an introduction to ONT data analysis with a focus in virus reconstruction. It includes 4 issues: basecalling, reads quality control, taxonomic assignation (diamond, kaiju and kraken2) and assemblies (incuding polishing/correction).


Linux and knowledge of NGS formats


  • Introduction to the principles of the technology (kits, flowcell)
  • Principles of basecalling
  • QC and data cleaning
  • taxonomic assignation with diamond and kaiju and vizualisation
  • Handling mapping and assembly tools suitable for ONT data
  • How to assemble a metagenome

Learning objectives

  • Understanding limits and advantages of ONT technology
  • Manipulating ONT data on a virtual machine on jupyter environment
  • Handling metagenomics tools to be able to analyse your own data

Training material


  • Julie Orjuela (JO) - UMR DIADE IRD
  • Denis Filloux (DF) - UMR PHIM IRD
  • Aurore Comte (AC) - UMR PHIM CIRAD


Date Location Topics Participants Instructors Links Units
2022 Burkina Faso Introduction to ONT data analyses for viruses 10 JO, DF, AC   UMR DIADE, PHIM