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 Galaxy-based framework dedicated to microbiota data analyses. ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.

A framework built on the shoulders of giants

To develop a modular, accessible, redistributable, sharable and user-friendly framework for scientist, we developed ASaiM using

  • Galaxy as the foundation

    Galaxy is a lightweight environment providing a simple graphical interface to bioinformatics tools, while automatically managing computation and data details. It improves the usability and reproducibility of biological studies.

  • Galaxy ToolShed, BioBlend and Ephemeris to install the tools, the worklows and the databases inside the Galaxy environment

  • Conda to install the tools and their dependencies

  • Docker to containerize and ship everything