Abstract
BackgroundThe 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/).ResultsWe 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).ConclusionsGmT 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.
Highlights
Reviewer Comments to Author: This manuscript is a resubmitted manuscript which describes a Galaxy wrapper of mothur, named Galaxy mothur Toolset (GmT)
I agree to the open peer review policy of the journal
I agree for my report to be made available under an Open Access Creative Commons CC-BY license
Summary
Reviewer Comments to Author: This manuscript is a resubmitted manuscript which describes a Galaxy wrapper of mothur, named Galaxy mothur Toolset (GmT). Title: Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur. The author answered all of my questions, and the manuscript is improved. 3: Line 42, 44, 45, and Figure 2 legend: KRONA --> Krona
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