title: Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS.
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.
authors: 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.
authors: Giovanni
authors: G
authors: Bacci
authors: 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.
authors: Alessia
authors: A
authors: Bani
authors: 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.
authors: Marco
authors: M
authors: Bazzicalupo
authors: 3. Department of Agrifood Production and Environmental Science, University of Florence, P.le delle Cascine 28, I-50144, Firenze, Italy.
authors: Maria Teresa
authors: MT
authors: Ceccherini
authors: 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.
authors: Marco
authors: M
authors: Galardini
authors: 3. Department of Agrifood Production and Environmental Science, University of Florence, P.le delle Cascine 28, I-50144, Firenze, Italy.
authors: Paolo
authors: P
authors: Nannipieri
authors: 3. Department of Agrifood Production and Environmental Science, University of Florence, P.le delle Cascine 28, I-50144, Firenze, Italy.
authors: Giacomo
authors: G
authors: Pietramellara
authors: 1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.
authors: Alessio
authors: A
authors: Mengoni
keywords: 16S rRNA; OTU clustering; bacterial communities.; metabarcoding; ribosomal database project
references: Appl Environ Microbiol. 2006 Jul;72(7):5069-72
references: 16820507
references: Mol Ecol Resour. 2014 Mar;14(2):426-34
references: 24128146
references: Appl Environ Microbiol. 2014 Dec;80(24):7583-91
references: 25261520
references: Nucleic Acids Res. 2010 Dec;38(22):e200
references: 20880993
references: Nucleic Acids Res. 2013 Jan;41(Database issue):D590-6
references: 23193283
references: Appl Environ Microbiol. 2007 Aug;73(16):5261-7
references: 17586664
references: BMC Bioinformatics. 2012 Feb 14;13:31
references: 22333067
references: Appl Environ Microbiol. 2011 Jun;77(11):3846-52
references: 21460107
references: ISME J. 2012 Jan;6(1):183-94
references: 21677692
references: PLoS One. 2010 Oct 26;5(10):e15406
references: 21048977