Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur

• Published in: Gigascience Vol. 8; no. 2
• Main Authors: Hiltemann, Saskia D, Boers, Stefan A, van der Spek, Peter J, Jansen, Ruud, Hays, John P, Stubbs, Andrew P
• Format: Journal Article
• Language: English
• Published: United States Oxford University Press 01-02-2019
• Subjects: Bioinformatics; Computational Biology - methods; Galaxies; Gene sequencing; Microbiota - genetics; Microorganisms; RNA, Ribosomal, 16S; rRNA 16S; Sequence analysis; Sequence Analysis, DNA - methods; Software; Technical Note; Workflow; mothur; 16S rRNA gene sequence analysis; microbial classification
• ISSN: 2047-217X; 2047-217X
• DOI: 10.1093/gigascience/giy166

Abstract
Background
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/).
Results
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).
Conclusions
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.