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

Pericard (admin), Pierre; Dufresne, Yoann; Blanquart, Samuel; Touzet, Helene

Document type :

Communication dans un congrès avec actes

Title :

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

Author(s) :

Pericard (admin), Pierre [Auteur]

Bioinformatics and Sequence Analysis [BONSAI]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Dufresne, Yoann [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Blanquart, Samuel [Auteur]
Bioinformatics and Sequence Analysis [BONSAI]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]
Touzet, Helene [Auteur]

Bioinformatics and Sequence Analysis [BONSAI]
Centre de Recherche en Informatique, Signal et Automatique de Lille - UMR 9189 [CRIStAL]

Conference title :

JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques

City :

Lille

Country :

France

Start date of the conference :

2017-07-03

Publication date :

2017

English keyword(s) :

Metagenomics
16S rRNA
assembly
taxonomic assignment
algorithm

HAL domain(s) :

Informatique [cs]/Bio-informatique [q-bio.QM]

English abstract : [en]

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 ...
Show more >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 .Show less >

Language :

Anglais

Peer reviewed article :

Oui

Audience :

Nationale

Popular science :

Non

Collections :

Centre de Recherche en Informatique, Signal et Automatique de Lille (CRIStAL) - UMR 9189

Source :

Harvested from HAL

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