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

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 , Alessia Bani  2 , Marco Bazzicalupo  2 , Maria Teresa Ceccherini  3 , Marco Galardini  2 , Paolo Nannipieri  3 , Giacomo Pietramellara  3 , Alessio Mengoni  2
Affiliations

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 et al. J Genomics. .

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.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interest exists.

Figures

Figure 1
Figure 1
Effect of bootstrap cut-off thresholds on the number of reads. The percentage of trimmed reads assigned to each taxonomic level is reported versus RDP bootstrap cut-off values. Shaded lines correspond to the 95% confidence interval assuming normality.
Figure 2
Figure 2
Percentage of assigned reads with respect to bootstrap cut-off thresholds at the genus level. Plots report the assigned reads for all dataset analyzed. Shaded lines correspond to the 95% confidence interval assuming normality.
See this image and copyright information in PMC

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