Course Metagenomic methods for microbial ecologists

September 15-19 2014

Target audience

PhD students or researchers in microbial ecology. MSc studenst can be considered, need letter of reference.Basic bioinformatics knowledge is pre requisite.

Pre-course homework:

- REQUIRED: - beginners course in R, should take less than one day.

- PLUS: few papers to read (max 3), suggestions welcome.


day 1 15 sept


  • Welcome: Louise Vet (NIOO-director) or/and Jos Raaijmakers
  • Introduction : Eiko Kuramae & Bas Dutilh
  • Q&A setup Linux, R, and RStudio: Dei Elurbe (Radboudumc), Manoeli Lupatini (NIOO) and Noriko Cassman (NIOO)

Afternoon: Preprocessing & quality filtering: Mattias de Hollander (NIOO)

day 2 16 sept

Someone from Rob Finn’s group EBI

EBI metagenomics pipeline, minimum information criteria, data submission

day 3 17 sept

Statistics: Paul J. McMurdie (Stanford)

day 4 18 sept

Assembly: Daan Speth (RU) and Bas E. Dutilh (UU)

Evening: course dinner with speakers symposium

day 5 19 sept

Symposium at NIOO: Environmental Metagenomics.

For more information contact Bas Dutilh
Send an email to Barbara van Kampen with
- your first and last name
- institute
- dept.
- invoicing address
- email address
- why do you wish to participate (max 100 words)