Applied Metagenomics

IMPORTANT DATES for this Course
Deadline for applications: October 3rd 2022
Course date: October 10th - October 14th 2022

Candidates with adequate profile will be accepted in the next 72 hours after the application until we reach 20 participants.


Erik Hjerde has a background in biology with a PhD in Genomics. During his career he has been working mainly with prokaryotes with focus on genomics and transcriptomics. In the last years, the focus has moved more towards metagenomic analysis on communities from both the human host as well as from various ecological habitats. He is the head of one national (Norwegian) work package within ELIXIR, that focuses on providing bioinformatic end user support and training.

Affiliation: ELIXIR-NO, University of Tromsø, Tromsø, NO

Espen Robertson has a background in biology with a PhD in Metagenomics. While still doing some metagenomic research, his main focus recently has been database integrations and software development. Espen is involved in various ELIXIR projects involving sensitive data, pipeline prototyping, administration of the project and various other topics.

Affiliation: ELIXIR-NO, University of Tromsø, Tromsø, NO

Course description

This course will give a comprehensive introduction to the research field of metagenomics. It will cover the basic concepts of microbiome analysis of shotgun metagenomic data using state of the art bioinformatics (amplicon sequencing will not be covered). The analysis methods that are being introduced are generic for all types of microbiomes, but we will be using data from the human microbiome as showcases. The course will start with the main preprocessing steps of raw sequence data, before various downstream analysis will be covered separately. These include taxonomic analysis, assembly, binning, and finally functional analysis with focus on antibiotic resistance genes. The theoretical part for each topic will be introduced via lectures, followed by practical hands-on exercises.


The participants will have acquired a theoretical basis and practical experience to understand the basic concepts of metagenomic analysis in order to conduct academic studies related to microbiome samples. This includes:

- performing advanced downstream analysis on both taxonomic functional profiles
- performing quality control, assembly and binning of metagenomic sequence data
- performing functional analysis and resistome analysis of metagenomes

Target Audience

The course is intended for researchers and students that are, or are planning to work with data analysis of metagenomic data.


Detailed Program


Instituto Gulbenkian de Ciência,

Apartado 14, 2781-901 Oeiras, Portugal

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Last updated:September 5th 2022