The basic principles of metagenomics (MGX)

This workshop was given in April 2023. A PDF of the manual and a compressed directory with the workshop data can be found at the bottom of the page. For the full slides, see this link. 

Metagenomics is increasingly popular but can feel very overwhelming for beginners. Join the two-day workshop on April 24-25, where we will discuss the basic principles of shotgun metagenomics. This includes nomenclature, standard practices, what metagenomics can/cannot do, and getting some hands-on experience by running end-to-end analyses. For the latter, you have a choice to use the provided example data sets, or to bring your own data and consult with the instructors (Bram van Dijk and Pauline Buffard) on how to go about learning about your samples. On day two, you'll learn about the importance of horizontal gene transfer (HGT) in microbial evolution, the difficulties of detecting HGT, and how the right experimental design can go a long way to fix these issues. So, before Pauline and I leave Plön next summer, don't miss out on this opportunity to enhance your knowledge of metagenomics and horizontal gene transfer analysis!

Preliminary schedule:

Monday April 24th: 10:00-12.00
Practical room (lecture on MGX basics, discussion) - Bram van Dijk

Monday April 24th: 13:30-16.00
Lecture hall (hands-on) - Bram van Dijk, Pauline Buffard

Tuesday April 25th: 10:00-12:00
Practical room (lecture on HGT, discussion) - Bram van Dijk

Tuesday April 25th: 13:30-16:00
Lecture hall (hand-on) - Bram van Dijk, Pauline Buffard

Additional information

While this is a course on metagenomics, this is not necessarily a course on how to use a computer. Instead, we will focus on:

• The need to move beyond 16s sequencing

• Metagenomics nomenclature

• End-to-end analysis
  (from “are my reads any good?” to “I think I know what’s in my samples”)

• Horizontal gene transfer and other things you may detect with read mapping

We will not cover how to use Wallace, use the command line, or how to install bioinformatic tools. We have set up a simple way for everyone with a PC/laptop to get started without having to do most of that, because we want to focus on the science instead. If you are a beginner and want to be prepared, Youtube is your friend. Plus, Carsten Fortmann-Grote gives instructions on these and similar topics on a regular basis. 

If you have further questions, please contact vandijk@evolbio.mpg.de