2018 - GigaScience
Abstract
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).
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.
Keywords: metagenomics; metataxonomics; user-friendly; Galaxy; Docker; microbiota; training
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.
Keywords: metagenomics; metataxonomics; user-friendly; Galaxy; Docker; microbiota; training
Batut, B., Gravouil, K., Defois, C., Hiltemann, S., Brugère, J. F., Peyretaillade, E., & Peyret, P. (2018).
ASaiM: a Galaxy-based framework to analyze microbiota data.
GigaScience, 7(6), giy057.