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^1,2, Alessia Bani¹, Marco Bazzicalupo¹, Maria Teresa Ceccherini³, Marco Galardini^1*, Paolo Nannipieri³, Giacomo Pietramellara³, Alessio Mengoni^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.
3. Department of Agrifood Production and Environmental Science, University of Florence, P.le delle Cascine 28, I-50144, Firenze, Italy.
^* Present address: EMBL-EBI - European Bioinformatics Institute Wellcome Trust Genome Campus Hinxton, Cambridge CB10 1SD, UK.

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Citation:
Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A. 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; 3:36-39. doi:10.7150/jgen.9204. Available from http://www.jgenomics.com/v03p0036.htm

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, metabarcoding, ribosomal database project, OTU clustering, bacterial communities.