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Gigascience. 2018 Dec 28. doi: 10.1093/gigascience/giy166. [Epub ahead of print]

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

Author information

1
Erasmus University Medical Center Rotterdam, Department of Bioinformatics.
2
Erasmus University Medical Center Rotterdam, Department of Medical Microbiology and Infectious Diseases.
3
Regional Laboratory of Public Health Kennemerland, Department of Molecular Biology.

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 analysing the mothur MiSeq standard operating procedure (SOP) data set (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.

PMID:
30597007
DOI:
10.1093/gigascience/giy166

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