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

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 assignment...

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Main Authors:	Bacci, Giovanni, Bani, Alessia, Bazzicalupo, Marco, Ceccherini, Maria Teresa, Galardini, Marco, Nannipieri, Paolo, Pietramellara, Giacomo, Mengoni, Alessio
Format:	Online
Language:	English
Published:	Ivyspring International Publisher 2015
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316179/

id	pubmed-4316179
recordtype	oai_dc
spelling	pubmed-43161792015-02-04 Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS Bacci, Giovanni Bani, Alessia Bazzicalupo, Marco Ceccherini, Maria Teresa Galardini, Marco Nannipieri, Paolo Pietramellara, Giacomo Mengoni, Alessio Short Research Communication 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. Ivyspring International Publisher 2015-02-01 /pmc/articles/PMC4316179/ /pubmed/25653722 http://dx.doi.org/10.7150/jgen.9204 Text en © 2015 Ivyspring International Publisher. Reproduction is permitted for personal, noncommercial use, provided that the article is in whole, unmodified, and properly cited. See http://ivyspring.com/terms for terms and conditions.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Bacci, Giovanni Bani, Alessia Bazzicalupo, Marco Ceccherini, Maria Teresa Galardini, Marco Nannipieri, Paolo Pietramellara, Giacomo Mengoni, Alessio
spellingShingle	Bacci, Giovanni Bani, Alessia Bazzicalupo, Marco Ceccherini, Maria Teresa Galardini, Marco Nannipieri, Paolo Pietramellara, Giacomo Mengoni, Alessio Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
author_facet	Bacci, Giovanni Bani, Alessia Bazzicalupo, Marco Ceccherini, Maria Teresa Galardini, Marco Nannipieri, Paolo Pietramellara, Giacomo Mengoni, Alessio
author_sort	Bacci, Giovanni
title	Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
title_short	Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
title_full	Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
title_fullStr	Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
title_full_unstemmed	Evaluation of the Performances of Ribosomal Database Project (RDP) Classifier for Taxonomic Assignment of 16S rRNA Metabarcoding Sequences Generated from Illumina-Solexa NGS
title_sort	evaluation of the performances of ribosomal database project (rdp) classifier for taxonomic assignment of 16s rrna metabarcoding sequences generated from illumina-solexa ngs
description	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.
publisher	Ivyspring International Publisher
publishDate	2015
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316179/
_version_	1613183951953723392

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

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