Software Packages

Department of Quantitative Health Sciences
Mayo Clinic Research
Formerly known as the Department of Health Sciences Research

Related links: Division Overview R Shiny Applications


A Targeted RE-sequencing Annotation Tool that offers a comprehensive, open framework, end-to-end solution for analyzing and interpreting targeted re-sequencing data. TREAT encompasses sequence alignment, variant calling, variant annotation, variant filtering, and visualization in one comprehensive analytic workflow. The rich set of annotations provided by TREAT enables the filtering of detected variants based on their functional characteristics, and visualizations at the variant positions allow the investigators to closely examine the identified variants of interest. An Amazon Cloud Image of TREAT is provided for researchers with no access to local bioinformatics infrastructure with instructions given in the tutorial below. The source code for local installation is available via the link below.

Authors: Yan W. Asmann, Sumit Middha, Asif Hossain, Saurabh Baheti, Ying Li, High-Seng Chai, Zhifu Sun, Patrick H. Duffy, Ahmed A. Hadad, Asha Nair, Xiaoyu Liu, Yuji Zhang, Eric W. Klee, Jean-Pierre A. Kocher. [06/2011]

Publication: TREAT: a bioinformatics tool for variant annotations and visualizations in targeted and exome sequencing data

Page last modified: October 24, 2014