Computational Metagenomics (Advanced)

This course teaches state of the art computational methods for the analysis of metagenomic data. First, the fundamentals are discussed, then the topics are explored in depth with lectures by experts and practical exercises with real data.

Course coordinator(s)

  • Marnix Medema, Wageningen University (WUR)
  • Georg Zeller, Leiden University Medical Center (LUMC)
  • Jingyuan Fu, University Medical Centre Groningen (UMCG)

Course credits

1.0 ECTS for following the course.

Course description

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 and profiling tools and the use of metagenomic databases. To compare metagenomic features between samples and conditions, we will study various statistical techniques, including differential abundance/expression analysis, association analysis with metadata and machine learning approaches. Finally, we will explore several levels of functional metagenome annotation, including the identification of biosynthetic gene clusters, virulence factors and phages, and primary metabolism. We will close the course with a keynote lecture by a prominent scientist in the field. 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.

Learning objectives

The students will be provided with a theoretical basis, a variety of methods, and a computational hands-on experience to analyse metagenomic and metatranscriptomics data for the taxonomic and functional analysis of microbiomes.

In this course the students will learn to:

  • describe the advantages and limitations of different types of metagenomics data using short- and long-read sequencing, as well as metabarcoding;
  • process raw metagenomic data through assembly, binning and taxonomic assignment
  • evaluate the quality and limitations of raw and assembled omics data
  • annotate metagenomic assemblies and metagenome-assembled genomes for important functional traits related to primary and secondary metabolism, virulence factors and phages
  • analyse similarities and differences across samples, as well as potential causal links, using appropriate statistical techniques
  • interpret processed metagenomics data using domain knowledge, functional annotation and making use of relevant databases

Additional 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.


If you would like to join this course using a wildcard (more information on this topic soon on this website), please contact the community manager, Petra Aarnoutse.
Until the maximum number of wildcard spots is reached, you can register with a wildcard until September 2, 2024.

Always mention in your application from which academic group the wildcard comes. Your registration is only valid after confirmation from the community manager.


Early bird registration (until August 19, 2024)

  • € 250 (excl. VAT) for PhD/MSc students
  • € 375 (excl. VAT) for academic researchers (non-profit)
  • € 560 (excl. VAT) industry participants (for profit)

From August 20, 2024 onwards:

  • € 300 (excl. VAT) for PhD/MSc students
  • € 450 (excl. VAT) for academic researchers (non-profit)
  • € 665 (excl. VAT) industry participants (for profit)

Please note that this is a three-day course.

Course fees includes course materials and catering (coffee, tea and lunch)

You can register for the course by filling out this registration form

There is room for max. 25 participants.

Find general enrollment information here.