Erasmus University Medical Center Rotterdam, Department of Pathology, Bioinformatics group, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
Erasmus University Medical Center Rotterdam, Department of Medical Microbiology and Infectious Diseases, Dr. Molewaterplein 40, 3015 GD, Rotterdam, The Netherlands.
Gigascience. 2019 Feb 1;8(2). doi: 10.1093/gigascience/giy166.
The determination of microbial communities using the mothur tool suite (https://www.mothur.org) is well established. However, mothur requires bioinformatics-based proficiency in order to perform calculations via the command-line. Galaxy is a project dedicated to providing a user-friendly web interface for such command-line tools (https://galaxyproject.org/).
We have integrated the full set of 125+ mothur tools into Galaxy as the Galaxy mothur Toolset (GmT) and provided a set of workflows to perform end-to-end 16S rRNA gene analyses and integrate with third-party visualization and reporting tools. We demonstrate the utility of GmT by analyzing the mothur MiSeq standard operating procedure (SOP) dataset (https://www.mothur.org/wiki/MiSeq_SOP).
GmT is available from the Galaxy Tool Shed, and a workflow definition file and full Galaxy training manual for the mothur SOP have been created. A Docker image with a fully configured GmT Galaxy is also available.
使用 mothur 工具套件（https://www.mothur.org）来确定微生物群落已经得到了很好的建立。然而， mothur 需要基于生物信息学的专业知识才能通过命令行进行计算。Galaxy 是一个专门为提供此类命令行工具的用户友好的网络界面而设计的项目（https://galaxyproject.org/）。
我们已经将 mothur 的全套 125 多个工具集成到 Galaxy 中，作为 Galaxy mothur Toolset（GmT），并提供了一系列工作流程，以执行端到端 16S rRNA 基因分析，并与第三方可视化和报告工具集成。我们通过分析 mothur MiSeq 标准操作程序（SOP）数据集（https://www.mothur.org/wiki/MiSeq_SOP）来证明 GmT 的实用性。
GmT 可从 Galaxy Tool Shed 获取，并且已经为 mothur SOP 创建了一个工作流程定义文件和完整的 Galaxy 培训手册。一个带有完全配置的 GmT Galaxy 的 Docker 映像也可用。
