The purpose of this repository is consolidate scripts/pipelines developed and shared by UW-Madison microbiome community members. We hope this resource will support campus researchers with their data analysis.

If you would like to contribute, please follow this link to find a template on how to add your scripts to this site.

To access or add your CHTC/ HTcondor submit files to the centralized repository please click this link

If you have any questions, join the discussions at slack

Resources

McMahon Lab - GitHub

TaxAss github page

TaxAss is a Taxonomy Assignment workflow that lets you classify 16S datasets using two different taxonomy reference databases. TaxAss was developed so that the McMahon Lab’s Freshwater Training Set (the FreshTrain) could be used for taxonomy assignment alongside comprehensive databases like Greengenes or Silva. We believe TaxAss will also work with other custom databases (so if that’s you, get in touch!)
Contact Robin Rohwer