用于对由Illumina-Solexa新一代测序技术生成的16S rRNA宏条形码序列进行分类学归属的核糖体数据库项目（RDP）分类器性能评估

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

作者信息

Bacci Giovanni, Bani Alessia, Bazzicalupo Marco, Ceccherini Maria Teresa, Galardini Marco, Nannipieri Paolo, Pietramellara Giacomo, Mengoni Alessio

机构信息

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.

1. Department of Biology, University of Florence, via Madonna del Piano 6, I-50019 Sesto Fiorentino, Firenze, Italy.

出版信息

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

DOI:10.7150/jgen.9204

PMID:25653722

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4316179/

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.

摘要

在此，我们报告了一项基准测试，该测试通过使用Illumina读数，研究了RDP分类器工具的自展截断值在不同分类等级上的数据保留效果。研究结果为规划测序深度和分类学赋值中自展截断值的选择提供了指导。