Metagenome-atlas: Three commands to start analysing your metagenome data

08 December 2021
Cancellation deadline:
26 November 2021
Silas Kieser
Omics data analysis
0.25 credits

No future instance of this course is planned yet


Metagenomics transformed how we study microbiomes by enabling the analysis of entire microbial communities from diverse environments, without the need for culturing. Recent improvements in algorithms enabled the assembly of larger and larger contigs from metagenomes, which then can be clustered together to produce draft genomes of new species. In this way, an almost unimaginable number of genomes from uncultured microbes could be assembled. These genomes allow for dataset-specific taxonomic analysis and genome-resolved functional annotation of metagenomes.

In this course, we will familiarize the participants with the steps required in assembly-based metagenomics (assembly, binning, genome completeness estimation, taxonomic and functional annotation). In the hand-on session we will use metagenome-atlas, a pipeline which implements the most commonly used metagenomics tools in a single workflow allowing users to get started in three commands analyzing your metagenome data. Finally, we will show how to use the output of metagenome-atlas to answer scientific questions.


PhD students, postdocs and other researchers, from any scientific environment (academia, facilities, companies, etc.) interested in analysing metagenomics data with Metagenome-Atlas.

Learning outcomes

At the end of the course, the participants will be able to:

  • Describe the advantages and challenges of assembly-based metagenomics
  • Assemble genomes from metagenomic reads and estimate their quality
  • Quantify genomes in a dataset
  • Evaluate the results of the analyses


Knowledge / competencies

The participants should know what a fastq file is and how to run commands in bash. The participants should have some familiarity with R or Python, for instance be able to open a table in either of the languages.


For the hands-on-session we will provide a virtual environment with all software pre-installed. The participants should have a computer with a not-too old web browser. A wired connection to the internet improves the experience.


The registration fees for academics are 60 CHF and 300 CHF for for-profit companies.

You will be informed by email of your registration confirmation. Upon reception of the confirmation email, participants will be asked to confirm attendance by paying the fees within 5 days.

Deadline for free-of-charge cancellation is set to 24/11/2021. Cancellation after this date will not be reimbursed. Please note that participation in SIB courses is subject to our general conditions.

Venue and Time

This course will be streamed.

Additional information

Coordination: Valeria Di Cola

We will recommend 0.25 ECTS credits for this course (given a passed exam at the end of the course).

You are welcome to register to the SIB courses mailing list to be informed of all future courses and workshops, as well as all important deadlines using the form here.

Please note that participation in SIB courses is subject to our general conditions.

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