Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.
Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research.
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DOI：
10.1128/msystems.00127-16
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发表时间：
2017-01
期刊：
影响因子：
6.4
通讯作者：
Langille MG
中科院分区：
文献类型：
--
作者：
Comeau AM;Douglas GM;Langille MG
随着微生物组领域的不断发展，许多研究人员正在学习如何进行适当的微生物组实验。我们在这里概述了一种简化和定制的方法来处理样本，从详细的测序文库构建到逐步的生物信息学标准操作程序。这允许快速和可靠的微生物组分析，使研究人员能够更多地关注他们的实验设计和结果。我们的测序方案、生物信息学教程和捆绑软件可以通过Microbiome Helper免费获得。随着微生物组研究领域的不断发展，微生物组助手将更新新的协议、脚本和培训材料。以序列为基础研究微生物群的方法，如16S rRNA基因测序和元基因组学，正在揭示微生物分类群与无数因素之间的联系。这些方法的一个缺点是，必要的测序文库准备和生物信息学分析是复杂的和不断变化的，这可能是新进入该领域的研究人员的障碍。我们自始至终提供了进行微生物组实验的三个基本组成部分：第一，一个简化和逐步定制的基因测序协议，它需要有限的实验室设备，具有成本效益，并且已经在各种类型的样本上进行了彻底的测试和利用；第二，一系列脚本，以集成各种常用的生物信息学工具，这些工具可以作为独立安装或作为单个可下载的虚拟映像提供；以及第三，一套生物信息学工作流程和教程，为微生物组领域的新手提供逐步的指导和教育。这一资源将为那些新进入微生物组领域的人提供基础，并将提供急需的指导和最佳做法，以确保开展高质量的微生物组研究。所有协议、脚本、工作流程、教程和虚拟图像均可通过Microbiome Helper网站(https://github.com/mlangill/microbiome_helper/wiki).免费获取随着微生物组领域的不断发展，许多研究人员正在学习如何进行适当的微生物组实验。我们在这里概述了一种简化和定制的方法来处理样本，从详细的测序文库构建到逐步的生物信息学标准操作程序。这允许快速和可靠的微生物组分析，使研究人员能够更多地关注他们的实验设计和结果。我们的测序方案、生物信息学教程和捆绑软件可以通过Microbiome Helper免费获得。随着微生物组研究领域的不断发展，微生物组助手将更新新的协议、脚本和培训材料。
As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results. Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper. As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials. Sequence-based approaches to study microbiomes, such as 16S rRNA gene sequencing and metagenomics, are uncovering associations between microbial taxa and a myriad of factors. A drawback of these approaches is that the necessary sequencing library preparation and bioinformatic analyses are complicated and continuously changing, which can be a barrier for researchers new to the field. We present three essential components to conducting a microbiome experiment from start to finish: first, a simplified and step-by-step custom gene sequencing protocol that requires limited lab equipment, is cost-effective, and has been thoroughly tested and utilized on various sample types; second, a series of scripts to integrate various commonly used bioinformatic tools that is available as a standalone installation or as a single downloadable virtual image; and third, a set of bioinformatic workflows and tutorials to provide step-by-step guidance and education for those new to the microbiome field. This resource will provide the foundations for those newly entering the microbiome field and will provide much-needed guidance and best practices to ensure that quality microbiome research is undertaken. All protocols, scripts, workflows, tutorials, and virtual images are freely available through the Microbiome Helper website (https://github.com/mlangill/microbiome_helper/wiki). IMPORTANCE As the microbiome field continues to grow, a multitude of researchers are learning how to conduct proper microbiome experiments. We outline here a streamlined and custom approach to processing samples from detailed sequencing library construction to step-by-step bioinformatic standard operating procedures. This allows for rapid and reliable microbiome analysis, allowing researchers to focus more on their experiment design and results. Our sequencing protocols, bioinformatic tutorials, and bundled software are freely available through Microbiome Helper. As the microbiome research field continues to evolve, Microbiome Helper will be updated with new protocols, scripts, and training materials.