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

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.

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

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

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• Course outline and practical info
• Introduction to metagenomics
• Working with the command line
• Setting up the Amazon Cloud
• QC and trimming

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• Read-based analyses

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• Metagenome assembly
• Assembly QC

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• Genome-resolved metagenomics

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• MAG annotation and downstream analyses
• Closing remarks and open discussion