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ASaiM - an environment to analyze intestinal microbiota data

New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies.

We therefore developed ASaiM, an Open-Source framework dedicated to microbiota data analyses. ASaiM integrates a comprehensive set of microbiota related tools, predefined and tested workflows dedicated to microbiota analyses. ASaiM offers then sophisticated analyses to scientists without command-line knowledge and a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.

ASaiM is also available as a Docker Galaxy flavour, but tools and workflows can be tested here.

Read more on ASaiM's homepage or via its preprint


Several workflows has been developed for ASaiM and are available on