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v1.0.0 release of ASaiM framework, an open-source Galaxy-based opinionated framework dedicated to microbiota sequence analyses

Bérénice Batut; Clémence Defois; Kévin Gravouil; Jean-François Brugère; Eric Peyretaillade; Pierre Peyret

Nowadays, complex communities of microorganisms can be studied in depth with metagenomics and metatranscriptomics, driven by evolution of sequencing techniques. Indeed, these meta'omics techniques offer insight concerning structure and functions of the studied communities. Notwithstanding, analyses of raw microbiota sequencing data are difficult because of data size and so numerous available and needed tools for data processing.

To overcome these limitations, we have developed ASaiM, an open-source Galaxy-based opinionated framework. It is accessible via a web-based interface to help scientists in their microbiota sequence data analyses. And it comes with an heavy documentation available on With an expertly selected collection of tools, workflows and databases, the framework is dedicated particularly to taxonomic, metabolic and taxonomically related metabolic information from raw sequences. By its intrinsic modularity, ASaiM allows tunning of workflows, tool parameters and usable databases.

Here, we present the first stable release of ASaiM framework, a powerful tool to analyze shotgun raw sequence data from complex communities of microorganisms. This open-source and biologist-oriented solution enhances usability, reproducibility and transparency of such studies and their comparative analyses. 

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