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SortMeRNA: Metatranscriptome classification

http://bioinfo.lifl.fr/RNA/sortmerna/

Actively developed

Inria Evaluation Committee Criteria for Software Self-Assessment: A-4, SO-3, SM-3, EM-3, SDL-4, DA-4, CD-4, MS-4, TPM-4

SortMeRNA is a tool designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. The distribution includes curated ribosomal RNA databases. It is available for download from our website, or through the open web-based platform Galaxy. SortMeRNA was released in October 2012, and is used in production by Genoscope (French National Center for Sequencing) to process metatranscriptomic data. Moreover, it has already been integrated in two published computational pipelines (A comprehensive metatranscriptome analysis pipeline and its validation using human small intestine microbiota datasets. M. Leimena et al., BMC genomics, 2013)${}^{,}$ (Metagenome survey of a multispecies and algae-associated biofilm reveals key elements of bacterial-algae interactions in photobioreactors. I. Krohn-Molt et al. Applied and environmental microbiology, 2013) and have identified users in multiple research laboratories worldwide (Umeå University (Sweden), Leibniz Institute DSMZ (Germany), NGS department of Campus Science Support Facilities GmbH (Austria), Oxford Centre for Integrative Systems Biology (Great Britain), Laboratoire d'Ecologie Alpine (Grenoble), PRABI (Lyon), Wageningen University (Netherlands), ...).