GITAR: An Open Source Tool for Analysis and Visualization of Hi-C Data

• Published in: Genomics, proteomics & bioinformatics Vol. 16; no. 5; pp. 365 - 372
• Main Authors: Calandrelli, Riccardo, Wu, Qiuyang, Guan, Jihong, Zhong, Sheng
• Format: Journal Article
• Language: English
• Published: China Elsevier B.V 01.10.2018; Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA%Department of Computer Science and Technology, Tongji University, Shanghai 200092, China; Elsevier; Oxford University Press
• Subjects: Animals; Application Note; Chromatin - chemistry; Chromatin interaction; Computer Graphics; Genome; Genomics - methods; Hi-C data normalization; Humans; Mice; Pipeline; Processed Hi-C data library; Software; Topologically-associated domain; Processed Hi-C data library; Chromatin interaction; Hi-C data normalization; Pipeline; Topologically-associated domain
• ISSN: 1672-0229; 2210-3244
• DOI: 10.1016/j.gpb.2018.06.006

Interactions between chromatin segments play a large role in functional genomic assays and developments in genomic interaction detection methods have shown interacting topological domains within the genome. Among these methods, Hi-C plays a key role. Here, we present the Genome Interaction Tools and Resources (GITAR), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, and visualization, as well as analysis of topologically-associated domains (TADs). GITAR is composed of two main modules: (1) HiCtool, a Python library to process and visualize Hi-C data, including TAD analysis; and (2) processed data library, a large collection of human and mouse datasets processed using HiCtool. HiCtool leads the user step-by-step through a pipeline, which goes from the raw Hi-C data to the computation, visualization, and optimized storage of intra-chromosomal contact matrices and TAD coordinates. A large collection of standardized processed data allows the users to compare different datasets in a consistent way, while saving time to obtain data for visualization or additional analyses. More importantly, GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data. GITAR is publicly available at http://genomegitar.org as an open-source software.