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Updated: Jan 31, 2026

Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur
Saskia D Hiltemann1, Stefan A Boers2, Peter J van der Spek1
1Erasmus University Medical Center Rotterdam, Department of Pathology, Bioinformatics group, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
The Galaxy mothur Toolset (GmT) simplifies microbial community analysis by integrating mothur tools into a user-friendly Galaxy interface, making complex bioinformatics accessible. This enhances microbial community determination and 16S rRNA gene analysis for researchers.
Area of Science:
- Microbiology
- Bioinformatics
- Computational Biology
Background:
- The mothur tool suite is a standard for microbial community analysis but requires command-line proficiency.
- Galaxy offers a user-friendly web interface for bioinformatics tools, simplifying complex analyses.
Purpose of the Study:
- To integrate the comprehensive mothur tool suite into the Galaxy platform.
- To develop user-friendly workflows for end-to-end microbial community analysis, including 16S rRNA gene sequencing data.
Main Methods:
- Integration of over 125 mothur tools into the Galaxy environment, creating the Galaxy mothur Toolset (GmT).
- Development of standardized workflows for 16S rRNA gene analysis within Galaxy.
- Demonstration of GmT utility using the mothur MiSeq Standard Operating Procedure (SOP) dataset.
Main Results:
- Successful integration of mothur tools into Galaxy, forming the Galaxy mothur Toolset (GmT).
- Established end-to-end workflows for 16S rRNA gene analyses and integration with visualization tools.
- Validated GmT performance using the established mothur MiSeq SOP dataset.
Conclusions:
- GmT enhances accessibility to advanced microbial community analysis tools.
- GmT is available via the Galaxy Tool Shed with comprehensive documentation and a Docker image for easy deployment.
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