• Advanced Courses in Life Sciences

    Header of Genetics and Genomics at Transmitting Science

Online Course – 1st Edition

Introduction to Genome-resolved Metagenomics for Microbial Communities

February 8th-12th, 2021

Genetics and Genomics

Genetics and Genomics


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This course will be delivered live online

24 hours of online live lessons. There are SCHOLARSHIPS AVAILABLE for this course. To apply, please REGISTER for the course and then FILL IN THE FORM HERE.

Course Introduction to Genome-resolved Metagenomics for Microbial Communities

Course Overview

Shotgun metagenomics, the non-targeted sequencing of genomes from all microorganisms in a sample, has brought new insights into microbial ecology. However, the limited length of individual metagenomic reads (far smaller than individual genes) is limiting downstream analyses, stressing the need to reconstruct reads and make sense of this output. On this front, genome-resolved metagenomics has emerged as a highly effective way to identify genomes directly from the metagenomic assembly outputs, bypassing cultivation to explore the gene content of individual microbial populations. With the ever-increasing use of applying next generation sequencing technologies to an array of environmental samples (e.g., microbiomes, oceans, soils), genome-resolved metagenomics has gained increased attention. Reconstructing and analysing genomes using metagenomic data as a starting point can be incredibly informative, but requires the understanding of key biological concepts (e.g., what is a bacterial population) and learning of bioinformatics tools (e.g., how to handle metagenomic assemblies and curate individual genomes).

This course will cover both the biological concepts and bioinformatics tools to take best advantage of the rapidly growing field of genome-resolved metagenomics. Participants will also briefly be introduced to the analysis of micro-diversity through single-nucleotide variants and processing of pangenomes to take best advantage of newly characterised genomes. Course material will be based on a mixture of lectures and hands-on exercises with real datasets for participants to practice on. The course is intended for researchers and graduate students who plan on studying microorganisms with metagenomics, and are especially interested in genomics through genome-resolved metagenomics.

Participants should expect to gather a good understanding of genome-resolved metagenomics, which they will be able to apply to their own metagenomic datasets.


Graduate or postgraduate degree in Biology, Life or Earth Sciences, familiarity with the UNIX terminal environment. Participants must have a personal computer (Windows, Mac, Linux) and access to a good internet connection. The use of a webcam and headphones is strongly recommended.

Participants are expected to have anvi’o installed in their own computer ahead of the start of the course (http://merenlab.org/2016/06/26/installation-v2), but support for troubleshooting will be provided ahead of the course. Ideally, participants should already have generated or are in the process of generating their own metagenomic datasets that will require the analysis mentioned in this workshop. However, this is not required, since reference data will be shared with all participants to perform the exercises.

A good internet connection is required to follow the course.




February 8th-12th, 2021

Schedule and Course length

Online live sessions from Monday 8th, Tuesday 9th, Thursday 11th and Friday 12th of February: from 10:00 to 12:00 and from 13:30 to 17:30 (GMT+1, Madrid time zone).

On Thursday 4th of February, there is a pre-course session from 15:00 to 16:00 for troubleshooting with anvi’o installation (this session is not mandatory)

24 hours live online.

This course is equivalent to 1 ECTS (European Credit Transfer System) at the Life Science Zurich Graduate School.

The recognition of ECTS by other institutions depends on each university or school.




Places are limited to 16 participants and will be occupied by strict registration order.

Participants who have completed the course will receive a certificate at the end of it.

Anna Fotaki Instructor for Transmitting Science

Dr. Anna Fotaki
University of Copenhagen

Tom Delmont instructor for Transmitting Science

Dr. Tom Delmont
Genoscope, CEA – CNRS


Thursday, February 4th (optional 1hr session)

Installation of anvi’o – troubleshooting

Monday, February 8th

Introduction to biological concepts

Introduction to bioinformatics tools

Tuesday, February 9th

Introduction to the anvi’o interface

Data visualisation

Wednesday, February 10th  

Day off

Thursday, February 11th

Extracting genomes from TARA Oceans

Analysing genomes

Friday, February 12th

Open discussions on special topics linked to the participants’ interests

Summary of the week


  • Course Fee
  • Early bird (until December 31st, 2020):
  • 440 € *

    (352 € for Ambassador Institutions)

  • Regular (after December 31st, 2020):
  • 575 € *

    (460 € for Ambassador Institutions)

  • Prices are VAT included.
    * Participants from companies/industry will have an extra charge of 100 €.

You can check the list of Ambassador Institutions. If you want your institution to become a Transmitting Science Ambassador please contact us at communication@transmittingscience.com


Discounts are not cumulative and apply only on the Course Fee. We offer the possibility of paying in two instalments (contact courses@transmittingscience.com).

Former participants will have a 5 % discount on the Course Fee.

20 % discount on the Course Fee is offered for members of some organizations (Ambassador Institutions). If you want to apply to this discount please indicate it in the Registration form (proof will be asked later).

Unemployed scientists living in the country were the course will be held, as well as PhD students based in that country without any grant or scholarship to develop their PhD, could benefit from a 40 % discount on the Course Fee. If you want to ask for this discount, please contact the course coordinator. That would apply for a maximum of 2 places and they will be covered by strict inscription order.


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