Environmental Metagenomics

Dates

4-8 April 2022

Due to the COVID-19 outbreak, this course will be held online

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 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

Program

Monday - 9 am -4 pm Berlin time  

    Introduction to metagenomics
    Working with the command line
    QC and trimming



Tuesday - 9 am -4 pm Berlin time  

    Read-based analyses
        Taxonomic annotation of metagenomes
        Functional annotation of metagenomes



Wednesday - 9 am -4 pm Berlin time  

    Metagenome assembly
    Assembly QC



Thursday - 9 am -4 pm Berlin time  

    Genome-resolved metagenomics in anvi'o



Friday - 9 am -4 pm Berlin time  

    Annotation of metagenome-assembled genomes (MAGs) and downstream analyses

Instructors

 

 

Dr. Antti Karkman

 

 

 

 

COst overview


Cancellation Policy:

 

 

 

> 30  days before the start date = 30% cancellation fee

 

< 30 days before the start date= No Refund.

 

 

 

Physalia-courses cannot be held responsible for any travel fees, accommodation or other expenses incurred to you as a result of the cancellation.