Computational Metagenomics (Advanced)

Course coordinators

  • Marnix Medema, Wageningen University
  • Jingyuan Fu, University Medical Centre Groningen


  • Marnix Medema, Wageningen University
  • Jingyuan Fu, University Medical Centre Groningen
  • Walter Pirovano, Baseclear
  • Vittorio Tracanna, University of Cologne
  • Mattias den Hollander, Netherlands Institute of Ecology
  • Saskia Hiltemann, Erasmus Medical Center
  • Tatiana Gurbich, European Bioinformatics Institute
  • Anne Kupczok, Wageningen University
  • Chrats Melkonian, Wageningen University / Utrecht University
  • Daniel Garza, Catholic University of Leuven
  • Melanie Schirmer, Technical University of Munich

Course credits

1.0 ECTS

Course overview

This course teaches state-of-the-art computational methods for the analysis of metagenome data. Lectures will be combined with hands-on computer sessions using Linux command line tools, Galaxy and R to practice use of the methods on real data. The course will start with foundational knowledge and skills in experimental design, sequencing technologies, quality control, assembly and binning. Subsequently, we will look at various taxonomic assignment algorithms and the use of metagenomic databases such as MGnify. To compare metagenomic features between samples and conditions, we will study various statistical techniques, including differential abundance/expression analysis, association analysis with metadata and causal inference. Finally, we will explore several levels of functional metagenome annotation, including the identification of biosynthetic gene clusters, virulence factors and phages, and community-level metabolic modeling. We will close the course with a keynote lecture on the use of metatranscriptomics to analyse gene expression patterns in microbiomes. After the course, the slides of the presentations and the practicals will remain available for future reference. Software packages used are freeware.

Target audience

Participants for the computational metagenomics course should have some general knowledge on next-generation sequencing (NGS) and should be familiar with basic Linux command line usage. The course is aimed at PhD students and postdocs, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend.

More information

Software used in the computer labs to install on your own computer will be made available before the start of the course.

For more information about the course you can contact Marnix Medema or  Jingyuan Fu.


The registration fees for this 3-day course are:

  • PhD student: 240 euro (excl. VAT)
  • Academic researcher (PI/Postdoc): 360 euro (excl. VAT)
  • Industry: 540 euros (excl.VAT)

The course fee includes:

  • Course material
  • Catering: coffee, tea and lunch will be provided.

There is room for max. 25 participants.

You can register via the registration form

Find general enrollment information here