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Deep dive into metagenomic data using metagenome-atlas and MMseqs2


Wednesday, 2nd September


13:30 to 16:30 (CEST)


  • Silas Kieser | PHYME, University of Geneva, Switzerland
  • Milot Mirdita | MPI for Biophysical Chemistry, Germany
  • Martin Steinegger | Seoul National University, Korea
  • Johannes Söding | MPI for Biophysical Chemistry, Germany
  • Sofie Thijs | Hasselt University, Belgium


In this tutorial, we will give an introduction in two ways of analysis of metagenomes

1. A genome centric approach using metagenome-atlas, a pipeline that combines the most commonly used steps (assembly, bin, genome- completeness estimation, taxonomic and functional annotation) in a single workflow and allows to get started in only three commands.

2. A gene centric analysis on the protein level using efficient protein-level assembly (Plass), ultra-fast protein clustering (Linclust), deep annotation by sensitive homology search as well as building goal-specific custom pipelines (MMseqs2).

The participants will:

1. Learn to assemble genomes from metagenomic reads and estimate their quality

2. Learn to assemble genes from metagenomic reads, cluster and annotate them using Plass, Linclust and MMseqs2

Target audience

Bioinformaticians comfortable with command line usage and basics of shell scripting.

Maximum participants



The tutorial is based on Jupiter notebooks. In order to be able to run the notebooks the participants should install anaconda ( and have a modern web browser installed. The Tutorial works on all unix systems (Linux, Mac and Windows Subsystem for Linux).


Time (CEST)
13:30 - 13:40 Introduction to the tutorial
13:40 - 14:00 Introduction to metagenomics
14:00 - 15:00 Warmer Activity
15:00 - 15:20 Break
15:20- 16:20 Mmseqs2 Tutorial
16:20 - 16:30 Conclusions