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...

Descripción completa

Detalles Bibliográficos
Autores principales: Bacci, Giovanni, Bani, Alessia, Bazzicalupo, Marco, Ceccherini, Maria Teresa, Galardini, Marco, Nannipieri, Paolo, Pietramellara, Giacomo, Mengoni, Alessio
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Ivyspring International Publisher 2015
Materias:
Short Research Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316179/
https://www.ncbi.nlm.nih.gov/pubmed/25653722
http://dx.doi.org/10.7150/jgen.9204
_version_ 1782355546193526784
author Bacci, Giovanni
Bani, Alessia
Bazzicalupo, Marco
Ceccherini, Maria Teresa
Galardini, Marco
Nannipieri, Paolo
Pietramellara, Giacomo
Mengoni, Alessio
author_facet Bacci, Giovanni
Bani, Alessia
Bazzicalupo, Marco
Ceccherini, Maria Teresa
Galardini, Marco
Nannipieri, Paolo
Pietramellara, Giacomo
Mengoni, Alessio
author_sort Bacci, Giovanni
collection PubMed
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.
format Online
Article
Text
id pubmed-4316179
institution National Center for Biotechnology Information
language English
publishDate 2015
publisher Ivyspring International Publisher
record_format MEDLINE/PubMed
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 J Genomics 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.
spellingShingle Short Research Communication
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
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_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_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_sort evaluation of the performances of ribosomal database project (rdp) classifier for taxonomic assignment of 16s rrna metabarcoding sequences generated from illumina-solexa ngs
topic Short Research Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4316179/
https://www.ncbi.nlm.nih.gov/pubmed/25653722
http://dx.doi.org/10.7150/jgen.9204
work_keys_str_mv AT baccigiovanni evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT banialessia evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT bazzicalupomarco evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT ceccherinimariateresa evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT galardinimarco evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT nannipieripaolo evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT pietramellaragiacomo evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs
AT mengonialessio evaluationoftheperformancesofribosomaldatabaseprojectrdpclassifierfortaxonomicassignmentof16srrnametabarcodingsequencesgeneratedfromilluminasolexangs

Ejemplares similares