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bioRxiv · 10.1101/259515

GITAR: An open source tool for analysis and visualization of Hi-C data

Calandrelli, R.·Wu, Q.·Guan, J.·Zhong, S.
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Abstract

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 GITAR (Genome Interaction Tools and Resources), a software to perform a comprehensive Hi-C data analysis, including data preprocessing, normalization, visualization and topologically associated domains (TADs) analysis. GITAR is composed of two main modules: 1) HiCtool, a Python library to process and visualize Hi-C data, including TADs 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 topological domain coordinates. A large collection of standardized processed data allows to compare different datasets in a consistent way and it saves time of work to obtain data for visualization or additional analyses. GITAR enables users without any programming or bioinformatic expertise to work with Hi-C data and it is freely available for the public at http://genomegitar.org as an open source software.

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Calandrelli, R., Wu, Q., Guan, J., Zhong, S.. 2018-02-04. GITAR: An open source tool for analysis and visualization of Hi-C data. https://doi.org/10.1101/259515

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