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

Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A - J Genomics (2015)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.


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.
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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.

Mentions: The assignments trend at the genus level (the lower taxonomic level that can be obtained using the RDP Classifier) was then inspected (Figure 2). Here also, V3 region better performed than V4 and V6 region in the retention of taxonomic information lowering bootstrap values, especially at bootstrap cutoff value of 0.5 and lower. A pseudo-fit of curve was also produced (Supplementary Material: Figure S1), which may allow researchers to infer the percentage of sequences that could be assigned to the genus level at different RDP bootstrap cut-offs.


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

Bacci G, Bani A, Bazzicalupo M, Ceccherini MT, Galardini M, Nannipieri P, Pietramellara G, Mengoni A - J Genomics (2015)

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.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC4316179&req=5

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.
Mentions: The assignments trend at the genus level (the lower taxonomic level that can be obtained using the RDP Classifier) was then inspected (Figure 2). Here also, V3 region better performed than V4 and V6 region in the retention of taxonomic information lowering bootstrap values, especially at bootstrap cutoff value of 0.5 and lower. A pseudo-fit of curve was also produced (Supplementary Material: Figure S1), which may allow researchers to infer the percentage of sequences that could be assigned to the genus level at different RDP bootstrap cut-offs.

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: 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.

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.

No MeSH data available.