Department of Structural Biology, Vlaams Instituut voor Biotechnologie (VIB), Pleinlaan 2, Brussels, 1050, Belgium.
Department of Bioscience Engineering, Vrije Universiteit Brussel, Pleinlaan 2, Brussels, 1050, Belgium.
Microbiome. 2014 Sep 30;2(1):30. doi: 10.1186/2049-2618-2-30.
16S ribosomal DNA (rDNA) amplicon sequencing is frequently used to analyse the structure of bacterial communities from oceans to the human microbiota. However, computational power is still a major bottleneck in the analysis of continuously enlarging metagenomic data sets. Analysis is further complicated by the technical complexity of current bioinformatics tools.
Here we present the less operational taxonomic units scripts (LotuS), a fast and user-friendly open-source tool to calculate denoised, chimera-checked, operational taxonomic units (OTUs). These are the basis to generate taxonomic abundance tables and phylogenetic trees from multiplexed, next-generation sequencing data (454, illumina MiSeq and HiSeq). LotuS is outstanding in its execution speed, as it can process 16S rDNA data up to two orders of magnitude faster than other existing pipelines. This is partly due to an included stand-alone fast simultaneous demultiplexer and quality filter C++ program, simple demultiplexer (sdm), which comes packaged with LotuS. Additionally, we sequenced two MiSeq runs with the intent to validate future pipelines by sequencing 40 technical replicates; these are made available in this work.
We show that LotuS analyses microbial 16S data with comparable or even better results than existing pipelines, requiring a fraction of the execution time and providing state-of-the-art denoising and phylogenetic reconstruction. LotuS is available through the following URL: http://psbweb05.psb.ugent.be/lotus .
16S 核糖体 DNA（rDNA）扩增子测序常用于分析从海洋到人类微生物群的细菌群落结构。然而，计算能力仍然是分析不断扩大的宏基因组数据集的主要瓶颈。当前生物信息学工具的技术复杂性进一步增加了分析的复杂性。
我们在这里介绍了 less operational taxonomic units scripts（LotuS），这是一种快速且用户友好的开源工具，用于计算去噪、去嵌合体检查、操作分类单元（OTUs）。这些是从多路复用、下一代测序数据（454、illumina MiSeq 和 HiSeq）生成分类丰度表和系统发育树的基础。LotuS 的执行速度非常快，因为它可以处理 16S rDNA 数据的速度比其他现有管道快两个数量级。这部分是由于包含一个独立的快速同步解复用器和质量过滤器 C++程序，简单解复用器（sdm），它与 LotuS 一起打包。此外，我们对两个 MiSeq 运行进行了测序，旨在通过对 40 个技术重复进行测序来验证未来的管道；这些都在这项工作中提供。
我们表明，LotuS 分析微生物 16S 数据的结果与现有管道相当，甚至更好，所需的执行时间更少，并提供了最新的去噪和系统发育重建。LotuS 可通过以下网址获得：http://psbweb05.psb.ugent.be/lotus。
