Dive into state-of-the-art computational methods for the analysis of metagenomic and metatranscriptomic data, from experimental design through to functional annotation of microbiomes. First, the fundamentals are discussed, then the topics are explored in depth with lectures by experts and practical exercises with real data.
Registration for this course has been closed, since we reached the maximum number of participants.
Course coordinators
- Prof. dr. Marnix Medema, Wageningen University (WUR)
- Dr. Georg Zeller, Leiden University Medical Center (LUMC)
- Prof. dr. Jingyuan Fu, University Medical Center Groningen (UMCG)
Course credits
Students receive 1.0 ECTS credits for following the course (3 consecutive days).
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 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 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.
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
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.
Detailed course program
Daily schedule of the course.
Additional information
For more information, contact Marnix Medema.
Wildcards
If you would like to join this course using a wildcard, please contact the BioSB community manager. You can register with a wildcard until 14 September 2026, or until the maximum number of wildcard spots is reached, whichever comes first. Please always state in your application which academic group issued the wildcard and attach the wildcard certificate. Your registration is only valid after confirmation from the community manager.
Registration
Early bird registration (until 31 August 2026):
- € 250 (excl. VAT) for PhD/MSc students
- € 375 (excl. VAT) for academic researchers (non-profit)
- € 560 (excl. VAT) industry participants (for profit)
From 1 September 2026 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. The ourse fee includes course materials and catering (coffee, tea and lunch).
Registration for this course has been closed, since we reached the maximum number of participants.
Find general enrollment information here.
