Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

BMC Bioinformatics

Research Article

Jose R Valverde¹  Rafael P Mellado¹  Jorge Barriuso¹ 

[1] Centro Nacional de Biotecnología (CSIC), c/Darwin 3, 28049, Madrid, Spain;

关键词: Multiple Sequence Alignment;    Glyphosate;    Distance Calculation;    Pairwise Alignment;    Short Length Sequence;   

DOI  :  10.1186/1471-2105-12-473

 received in 2011-11-03, accepted in 2011-12-14,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundNext generation sequencing (NGS) enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple and complex workflows, including frequently used as well as recently published tools, and report on their respective accuracy and efficiency under various conditions covering different sequence lengths, number of sequences and real world experimental data from rhizobacterial populations of glyphosate-tolerant maize treated or untreated with two different herbicides representative of differential diversity studies.ResultsAlignment and distance calculations affect OTU estimations, and multiple sequence alignment exerts a major impact on the computational time needed. Generally speaking, most of the analyses produced consistent results that may be used to assess differential diversity changes, however, dataset characteristics dictate which workflow should be preferred in each case.ConclusionsWhen estimating bacterial diversity, ESPRIT as well as the web-based workflow, RDP pyrosequencing pipeline, produced good results in all circumstances, however, its computational requirements can make method-combination workflows more attractive, depending on sequence variability, number and length.

【 授权许可】

Unknown   
© Barriuso et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.