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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 participants will need to bring their own notebooks with a modern web browser installed (we recommend Firefox). We will provide a web-based shell to access the required software and data on our servers.