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  • The Inria's Research Teams produce an annual Activity Report presenting their activities and their results of the year. These reports include the team members, the scientific program, the software developed by the team and the new results of the year. The report also describes the grants, contracts and the activities of dissemination and teaching. Finally, the report gives the list of publications of the year.

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Section: New Software and Platforms


Mapping-Assisted Targeted-Assembly for Metagenomics

Keywords: Metagenomics - Genome assembling - Graph algorithmics

Scientific Description: MATAM relies on the construction of a read overlap graph. Overlaps are computed using SortMeRNA. The overlap graph is simplified into relevant components related to specific and conserved regions. Components are assembled into contigs using SGA and contigs are finally assembled into scaffolds. The process yields nearly full length marker sequences with a very low error rate compared to the state of the art approaches. Taxonomic assignation of the obtained scaffolds is performed using the RDP classifier and is represented using Krona.

Functional Description: MATAM provides targeted genes assembly from the short metagenomic reads issued from environmental samples sequencing. Its default application focuses on the gold standard for species identification, 16S / 18S ribosomal RNA SSU genes. The produced gene scaffolds are highly accurate and suitable for precise taxonomic assignation. The software also provides a RDP classification for the reconstructed scaffolds as well as an estimation of the relative population sizes.