Background: New generations of sequencing platforms coupled to numerous bioinformatics tools have 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. Findings: We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota data analyses. ASaiM provides an extensive collection of tools to assemble, extract, explore, and visualize microbiota information from raw metataxonomic, metagenomic, or metatranscriptomic sequences. To guide the analyses, several customizable workflows are included and are supported by tutorials and Galaxy interactive tours, which guide users through the analyses step by step. ASaiM is implemented as a Galaxy Docker flavour. It is scalable to thousands of datasets but also can be used on a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io). Conclusions: Based on the Galaxy framework, ASaiM offers a sophisticated environment with a variety of tools, workflows, documentation, and training to scientists working on complex microorganism communities. It makes analysis and exploration analyses of microbiota data easy, quick, transparent, reproducible, and shareable.

Additional Metadata
Keywords Docker, Galaxy, Metagenomics, Metataxonomics, Microbiota, Training, User-friendly
Persistent URL dx.doi.org/10.1093/gigascience/giy057, hdl.handle.net/1765/109683
Journal GigaScience
Citation
Batut, B. (Bérénice), Gravouil, K. (Kévin), Defois, C. (Clémence), Hiltemann, S, Brugère, J.-F. (Jean-François), Peyretaillade, E. (Eric), & Peyret, P. (Pierre). (2018). ASaiM: A Galaxy-based framework to analyze microbiota data. GigaScience, 7(6). doi:10.1093/gigascience/giy057