To understand a microbiota environment, we need answers to questions as “Who is there?”, “What are they doing?” and “How are they doing it?”. This can be achieved by analysis of metagenomic and metatranscriptomic sequences sampled from interesting environment.

These analyses often follow the same scheme (with some variation given the sequences, the questions, ...): sequence pretreatments, taxonomic and functional assignations of the sequences. These analyses are complex and require numerous tools. ASaiM framework provides a Galaxy environment to help analyses of gut microbiota data with selected tools, databases and workflows.

In this tutorial, we explain how to use ASaiM framework to analyze metagenomic sequences of gut microbiota to obtain taxonomic and functional assignations of sequences.