Department of Biology, Institute of Microbiology and Swiss Institute of Bioinformatics, ETH Zürich, Zürich, Switzerland.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Curr Protoc. 2021 Aug;1(8):e218. doi: 10.1002/cpz1.218.
The mOTU profiler, or mOTUs for short, is a software tool that enables the profiling of microbial communities in terms of their taxonomic composition, relative abundance of metabolically active members, and diversity of strain populations. To this end, it maintains a database of single-copy phylogenetic marker gene sequences, which are used as a reference to which short read metagenomic and metatranscriptomic reads are mapped for the identification and quantification of microbial taxa. Here, we describe the most common use cases of the mOTU profiler in two basic protocols. Additional supporting protocols provide information on its installation and in-depth guidance on adjusting its settings for increasing or decreasing the stringency with which taxa are detected and quantified, as well as for customizing the output file format. Guidelines for understanding the profiling results are provided, along with additional information on unique features, methodological details, and the development history of the tool. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Metagenomic and metatranscriptomic mOTU profiling Basic Protocol 2: Metagenomic SNV profiling Support Protocol 1: Installing mOTUs Support Protocol 2: Profiling pipeline-step by step Support Protocol 3: The mOTUs profiling routine using advanced parameters Support Protocol 4: Metagenomic SNV calling: advanced parameters.
mOTU 分析器（简称 mOTUs）是一款软件工具，可根据分类组成、代谢活跃成员的相对丰度以及菌株群体的多样性来分析微生物群落。为此，它维护了一个单拷贝系统发育标记基因序列数据库，用于将短读测序宏基因组和宏转录组序列映射到微生物分类单元的鉴定和量化。在这里，我们在两个基本方案中描述了 mOTU 分析器的最常见应用案例。其他辅助方案提供了有关其安装的信息，并深入指导如何调整其设置，以增加或降低检测和量化分类单元的严格性，以及自定义输出文件格式。还提供了有关如何理解分析结果的指南，以及有关该工具的独特功能、方法细节和开发历史的其他信息。© 2021 作者。Wiley Periodicals LLC 出版的《当代协议》。基本方案 1：宏基因组和宏转录组 mOTU 分析基本方案 2：宏基因组单核苷酸变异（SNV）分析支持方案 1：mOTUs 的安装支持方案 2：分析流程分步指导支持方案 3：使用高级参数的 mOTUs 分析常规支持方案 4：宏基因组 SNV 调用：高级参数。
