Soyez le premier à aimer ceci
More information about the project are available at http://asaim.github.io/
Metatranscriptomic data allow active microbial communities description by gene products analysis. In comparison to metagenomic studies, few metatranscriptomic data have been obtained on environmental ecosystems (soil, water, mine drainage…) as on human-associated microbiota despite health concerns. This discrepancy is due to difficulties in RNA recovery but also to a lack of tools dedicated to metatranscriptomic data processing. Nevertheless, some homemade pipelines adapted from metagenomics analyses exist but are not freely available and thus not easily accessible. Here we present ASAIM (Auvergne Sequence Analysis for Intestinal Microbiota), a pipeline to process metatranscriptomic data from intestinal microbiota. Starting from raw reads, it generates taxonomic and functional assignments using databases dedicated to this microbiome. These gut databases become more and more supplied by large metagenomic projects (like MetaHIT and HMP projects for microbial reference genomes) and therefore useful for reliable and accurate assignments. Finally, ASAIM combines taxonomic, functional and abundance information, coupled to statistical analyses and data mining tools. This pipeline is designed to be adjustable (personalized or proposed data processing given the type of data) and intuitive with its web interface, documentation and tutorials. ASAIM is freely available at http://g2im.u-clermont1.fr/asaim/ and can be downloaded or directly interrogated through its web interface.