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Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics

Pierre Pericard 1, 2 Yoann Dufresne 1, 2 Samuel Blanquart 1, 2 Hélène Touzet 1, 2
2 BONSAI - Bioinformatics and Sequence Analysis
CNRS - Centre National de la Recherche Scientifique, CRIStAL - Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189, Université de Lille, Sciences et Technologies, Inria Lille - Nord Europe
Abstract : Advances in the sequencing of uncultured environmental samples, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution. We designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered genome fractions and is suitable to provide improved assemblies for precise taxonomic assignments .
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https://hal.inria.fr/hal-01574629
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Submitted on : Friday, September 29, 2017 - 12:46:29 PM
Last modification on : Thursday, June 17, 2021 - 4:32:02 PM
Long-term archiving on: : Saturday, December 30, 2017 - 1:22:28 PM

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Pierre Pericard, Yoann Dufresne, Samuel Blanquart, Hélène Touzet. Reconstruction of full-length 16S rRNA sequences for taxonomic assignment in metagenomics. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. ⟨hal-01574629⟩

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