Microbiome Platform Tools
The OSU Center of Microbiome Science supports a variety of applications for microbiome analyses through the Ohio Supercomputer Center (OSC).
To access these applications, you must have an OSC user account.
View the COMS_microbiome_applications and follow the following instructions to get started.
If you have questions, please contact the Ohio Supercomputer Center Virtual Help Desk or the Center of Microbiome Bioinformatics Helpline.
Instructions on how to use microbiome analysis tools available at OSC
The Microbiome Platform makes its programs and associated databases publicly available to all OSC users as applications and modules.
Once you've logged into OSC, activate the CoMS microbiome tools module system:
| module use /fs/ess/community/CoMS_microbiome_tools/sif-apps_staging/modulefiles
Once activated, you can view the CoMS microbiome tools, as well as others available system-wide on OSC:
| module avail
To use a CoMS microbiome tool, load the module similar to any OSC module:
| module load [tool]/[version]
This will display instructions for its use, as well as alternatives.
Additional information are available in the README file:
| cat /fs/ess/community/CoMS_microbiome_tools/README_usage
If a module or application does not work, or you do not see the one(s) that you want, please contact microbiome@osu.edu.
More resources
- Free Intro to R
- R Basics
- R for Data Science
- Learn Python
- Other Data Science Tutorials (Machine Learning, Data Visualization)
- Unix tutorial (basic commands in the terminal)
For plotting data
For 16S and Metagenomics
- Huttenhower lab tools (PICRUSt, GraPhlAn, MetaPhlAn, MetaPhlAn2, LEfSe, microPITA)
- MicrobiomAnalyst
- DADA2 tutorial
- Harnessing Our Inner Ecology to Track and Treat Disease: Free Virtual Course
- Offered by the Institute for Systems Biology, this course is available via YouTube and covers topics including:
- Analyzing amplicon sequencing data with QIIME2
- Modeling microbiota-wide metabolism with MICOM
- Defining a healthy gut microbiome: Insights from deeply phenotyped cohorts
- Offered by the Institute for Systems Biology, this course is available via YouTube and covers topics including:
For Metabolomics
For Multi-omics integration
For linking miRNA’s to targets and functions
For RNASeq gene-expression profiling
IVirus
Visit the iVirus website: https://www.ivirus.us/
Ohio State tools
- Microbiome Platform presented by IDI-GEMS and CoMS
- Microbial and Viral Ecological Research in Columbus Informatics (MAVERICs)
- CoMS Microbiome Working Group Webinars / Primers (coming soon!)
- CoMS Advanced Ecological Statistics Working Group Webinars / Primers (coming soon!)
- CoMS Viromics Working Group Webinars / Primers