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

ABSTRACT:

Background

Next 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.

Results

Alignment and distance calculations affect OTU estimations, and multiple sequence alignment exerts a major impact on the computational time

SUBMITTER: Barriuso J 

PROVIDER: S-EPMC3258296 | biostudies-literature | 2011 Dec

REPOSITORIES: biostudies-literature