Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS

Giovanni Bacci; Alessia Bani; Marco Bazzicalupo; Maria Teresa Ceccherini; Marco Galardini; Paolo Nannipieri; Giacomo Pietramellara; Alessio Mengoni

doi:10.7150/jgen.9204

Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS

J Genomics. 2015 Feb 1:3:36-9. doi: 10.7150/jgen.9204. eCollection 2015.

Authors

Giovanni Bacci¹, Alessia Bani², Marco Bazzicalupo², Maria Teresa Ceccherini³, Marco Galardini², Paolo Nannipieri³, Giacomo Pietramellara³, Alessio Mengoni²

Affiliations

¹ 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy. ; 2. Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Centro di Ricerca per lo Studio delle Relazioni tra Pianta e Suolo (CRA-RPS), Via della Navicella 2/4, I-00184 Roma, Italy.
² 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.
³ 3. Department of Agrifood Production and Environmental Science, University of Florence, P.le delle Cascine 28, I-50144, Firenze, Italy.

Abstract

Here we report a benchmark of the effect of bootstrap cut-off values of the RDP Classifier tool in terms of data retention along the different taxonomic ranks by using Illumina reads. Results provide guidelines for planning sequencing depths and selection of bootstrap cut-off in taxonomic assignments.

Keywords: 16S rRNA; OTU clustering; bacterial communities.; metabarcoding; ribosomal database project.