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

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Chromatin interactions are crucial for genomic functions.
• Hi-C technology enables detection of genome-wide interactions.
• Topologically-associated domains (TADs) are key structural units within the genome.

Purpose of the Study:

• To present GITAR, a comprehensive software suite for Hi-C data analysis.
• To provide tools for data preprocessing, normalization, visualization, and TAD analysis.
• To make Hi-C data analysis accessible to users with limited programming experience.

Main Methods:

• Development of GITAR, comprising HiCtool (Python library) and a processed data library.
• HiCtool guides users through a pipeline from raw Hi-C data to contact matrices and TAD coordinates.
• Standardized processing of human and mouse Hi-C datasets.

Main Results:

• GITAR facilitates step-by-step Hi-C data processing and analysis.
• The software enables computation, visualization, and storage of intra-chromosomal contact matrices and TADs.
• A curated library of processed datasets allows for consistent cross-dataset comparisons.

Conclusions:

• GITAR democratizes Hi-C data analysis, empowering researchers without bioinformatics expertise.
• The integrated tools and processed data accelerate genomic interaction studies.
• GITAR is available as open-source software, promoting wider adoption and research.