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Metagenomics approaches and data analysis

general information

  • Next occasion: March 31st - April 2nd, 2014 - register
  • Location: Nijmegen, The Netherlands
  • Organiser: CMBI & NBIC
  • Coordinators: Sacha van Hijum (Radboudumc/NIZO food research), Bas Dutilh (Radboudumc/CMBI), Celia van Gelder (NBIC)
  • Information about the 2014 edition of the metagenomics course can be found at the BioSB website




Below you will find information about the 2013 edition of the metagenomics course. You will find here the programme and slides from most lectures.

Specific information about 2013 edition of the course is available here.


The Metagenomics course is organised for the first time in 2013 and covers Metagenomics and metatranscriptomics of prokaryotes, eukaryotes and viruses. Topics are Metagenomics-specific issues like calling taxa, functional annotation, metagenome assembly and comparative Metagenomics. This advanced course is targeted at PhD students and researchers. Participants will be invited to introduce their own research questions. Towards the end of the course, remaining questions specific to your research will be discussed with the group.


  • Sacha van Hijum (NIZO food Research, CMBI)
  • Bas Dutilh (CMBI)
  • Johan den Dunnen (LUMC)
  • Willem de Vos (Wageningen University)
  • Harro Timmerman (NIZO food research)
  • Jos Boekhorst (NIZO food research)
  • Jeroen Laros (LUMC)
  • Victor de Jager (CMBI, Wageningen University)
  • Rutger Vos (Naturalis Biodiversity Center)
  • Jeroen Laros (LUMC)
  • Martijn Vermaat (LUMC)
  • Intawat Nookaew (Chalmers, Sweden)

Target audience

Participants of the NBIC Advanced NGS courses should preferably have participated in the general NGS data analysis course or otherwise have demonstrated hands-on experience with NGS data analysis. The course is aimed at PhD students and post-docs or researchers with a similar level, but scientific programmers and data analysts with a background in biology and bioinformatics may also attend.

Course Description

Metagenomics is one of the (many) applications of modern (Next-Gen) sequencing technologies, also called environmental genomics. By definition, metagenomics is the process of direct sequencing the DNA of an environmental sample, i.e. of a whole microbial community as it exists in nature, bypassing the need for cultering techniques.

This course will help participants answering questions like:

  • For what type of questions can metagenomics help?
  • What are possible approaches of metagenomics?
  • How to monitor and predict environmental conditions and change?
  • Biological insights, phylogenetic diversity.
  • Examining genes/operons for enzyme and natural products.

Many hurdles arise in the analysis and assembly of environmental genomics records, among which short sequence reads, high species complexity in samples and the availability of specialised software for microbial genomics analysis.

Among the many topics in metagenomics addressed in this course are:
experimental approaches; sequencing technologies; platforms and platform specific issues; methodologies; Sample preparation; QC-reports & quality controls; mapping sequence reads; taxonomic annotation; functional annotation & function determination; unknown gene prediction; comparative metagenomics; amplicon sequencing; shotgun metatranscriptomics; calling taxa; metagenome assembly; evaluation; visualisation and reporting of results; tools & algorithms; 16S profiling; databases; mapability; k-mer profiling; cross assembly; QIIME; MG-RAST; iPath.


Creative Commons License

Lecture notes (slides), Workshops and patricipants' presentations of the 2013 Metagenomics Course in Leiden

NBIC Advanced NGS Courses by Netherlands Bioinformatics Centre are licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at NBIC.

Day 1: Wednesday February 6th

Day 2: Thursday February 7th

Day 3: Friday February 8th