Section: New Software and Platforms

MATAM

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.

• Participants: Hélène Touzet, Pierre Pericard, Yoann Dufresne, Samuel Blanquart and Loïc Couderc

• Contact: Hélène Touzet

• Publication: MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes

• URL: https://github.com/bonsai-team/matam