GCC 2017 has ended
The 2017 Galaxy Community Conference (GCC2017) is being held in Montpellier, France, 26-30 June.  GCC2017 will include keynotes and accepted talks, poster sessions, demos, birds-of-a-feather meetups, exhibitors, and plenty of networking opportunities. There will also be three days of pre-conference activities, including hackathons and training. If you work in data-intensive biomedical research, there is no better place than GCC2017 to present your work and to learn from others.

The full printed program is also available.
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Thursday, June 29 • 15:40 - 17:00
P27: ASaiM: a Galaxy-based framework to analyze raw sequencing data from microbiota

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Poster (doi: 10.7490/f1000research.1114448.1)


Bérénice Batut 1*, Clémence Defois 2, Kévin Gravouil 2,3,4, Jean-François Brugère 2, Eric Peyretaillade 2, Pierre Peyret 2

1 : Bioinformatics Group, Department of Computer Science, University of Freiburg, Germany
2 : Microbiologie Environnement Digestif Santé - Clermont Auvergne  (MEDIS), INRA Clermont-Ferrand-Theix : UMR0454, Université Clermont Auvergne : UMR0454INRA, Centre de Recherches de Clermont-Ferrand - Theix / 63122 Saint-Genès Champanelle -  France
3 : Microorganismes : Génome et Environnement - Clermont Auvergne  (LMGE), Université Clermont Auvergne : UMR6023, Centre National de la Recherche Scientifique : UMR6023Campus des Cézeaux / 24, avenue des Landais BP 80026 / 63170 Aubière -  France
4 : Laboratoire dÍnformatique, de Modélisation et dÓptimisation des Systèmes - Clermont Auvergne  (LIMOS)SIGMA Clermont, Université Clermont Auvergne : UMR6158, Centre National de la Recherche Scientifique : UMR6158ISIMA / Campus des Cézeaux BP 10025 / 63173 AUBIERE cedex -  France* : Corresponding author

With the development of the new generation of sequencing platforms and the development of metagenomics and metatranscriptomics technologies, complex microorganism communities can be more easily studied. Numerous bioinformatics tools are available for such purpose but analyses of microbiota data remain difficult: numerous different bioinformatics tools must be combined to extract useful information. Indeed, modular, accessible and sharable user-friendly tools are then urgently needed to conduct efficient analyses to explore microbiota data. We developed then ASaiM, an open-source Galaxy-based framework dedicated to microbiota data analyses.

ASaiM provides an expertly selected collection of tools to exploit and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To help the analyses, several (customizable) workflows are included. The main workflow has been tested on two mock metagenomic datasets with controlled communities. More accurate and precise taxonomic analyses and more informative metabolic description have been obtained compared to EBI metagenomics' pipeline on the same datasets.

The available workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses. Furthermore, an effort on documentation of ASaiM, its tools and workflows has been made (http://asaim.readthedocs.io/).

Based on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge, while emphasizing reproducibility, customization and effortless scale up to larger infrastructures. ASaiM is implemented as Galaxy Docker flavour and can be easily extended with additional tools or workflows. ASaiM provides then a powerful framework to easily and quickly exploit microbiota data in a reproducible and transparent environment.

avatar for Bérénice Batut

Bérénice Batut

Post-doc, University of Freiburg
Bérénice is a post-doc in the Freiburg Galaxy Team (Backofen lab). She analyzes biological data (metagenomics, HTS data, evolution) and develops tools to facilitate data analysis, mainly for Galaxy.Bérénice is also passionate about training. She regularly gives workshops on data... Read More →

Thursday June 29, 2017 15:40 - 17:00 CEST
Le Corum Le Corum

Attendees (2)