Environmental metagenomics

Instructors

Dr. Antti Karkman, University of Helsinki
Dr. Igor Pessi, University of Helsinki

Overview

Metagenomics is a widely used tool for the analysis of microbial communities as it gives access to the genomes of uncultured microorganisms. Particularly in complex ecosystems (e.g. soil), currently uncultured taxa typically comprise a large fraction of the microbial communities. Metagenomics has many benefits compared to amplicon sequencing, as it gives information not only on the taxonomic diversity but also on the functional composition of microbial communities. Recent bioinformatic developments now allow the recovery of metagenome-assembled genomes (MAGs) at an incredible depth.

During this one week course you will learn state-of-the-art bioinformatic approaches to analyse metagenomic data. We will cover both both read- and assembly-based methods, focusing on the strenght of each of these methods depending on the research question. We will use data from both short- (e.g. Illumina) and long-read (e.g. Nanopore) sequencing platforms, as it improves dramatically MAG assembling and binning compared to short-read-only methods.

Prerequisites

We assume some basic awareness of analysis of UNIX and molecular biology.

Outcomes

By completing this course, you will:

Understand the basics of metagenomic sequencing and bioinformatic approaches to the analyis of metagenomic data
Be able to plan and execute a metagenomic sequencing project
Have an up-to-date knowledge on the bioinformatic tools and best practices for the analysis of metagenomes
Be able to choose the right tools and approaches to answer your specific research question
Have confidence to learn new methods needed to answer your research question