Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur. Issue 2 (28th February 2018)

• Record Type: Journal Article
• Authors: Hiltemann, Saskia D; Boers, Stefan A; van der Spek, Peter J; Jansen, Ruud; Hays, John P; Stubbs, Andrew P
• Is Part Of: GigaScience. Volume 8:Issue 2(2019)
• Publication Date: 2018-02-28
• Subjects: microbial classification -- 16S rRNA gene sequence analysis -- mothur; Information storage and retrieval systems -- Research -- Periodicals; Biology -- Research -- Periodicals; Medical sciences -- Research -- Periodicals; Database management -- Periodicals; 570.285
• DOI: 10.1093/gigascience/giy166
• Languages: English
• ISSNs: 2047-217X

Abstract

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.