MATAM is a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. It has been applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes.
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Pericard P, Dufresne Y, Couderc L, Blanquart S, Touzet H.
MATAM: reconstruction of phylogenetic marker genes from short sequencing reads in metagenomes.
Bioinformatics. 2018 Feb 15;34(4):585-591. doi: 10.1093/bioinformatics/btx644. PMID: 29040406.