We found a match
Your institution may have rights to this item. Sign in to continue.
- Title
Galaxy mothur Toolset (GmT): a user-friendly application for 16S rRNA gene sequencing analysis using mothur.
- Authors
Hiltemann, Saskia D; Boers, Stefan A; van der Spek, Peter J; Jansen, Ruud; Hays, John P; Stubbs, Andrew P
- 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%5fSOP). 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.
- Subjects
RIBOSOMAL RNA; RNA sequencing; MICROBIAL communities
- Publication
GigaScience, 2019, Vol 8, Issue 2, pN.PAG
- ISSN
2047-217X
- Publication type
Article
- DOI
10.1093/gigascience/giy166