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

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...

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Detalles Bibliográficos
Autores principales: Hiltemann, Saskia D, Boers, Stefan A, van der Spek, Peter J, Jansen, Ruud, Hays, John P, Stubbs, Andrew P
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2018
Materias:
Technical Note
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377400/
https://www.ncbi.nlm.nih.gov/pubmed/30597007
http://dx.doi.org/10.1093/gigascience/giy166
Descripción
Sumario: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.

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