hictk

hictk processes Hi-C .hic and .cool contact/interaction matrix files and provides high-performance conversion and processing routines for genome organization studies.

Key Features:

• Dual Format Support: Native support for both .hic and .cool file formats to operate directly on common Hi-C binary formats.
• Performance Optimization: Implemented in C++ to deliver high-speed processing performance for large Hi-C datasets.
• Multi-Language Compatibility: Exposes Python and R bindings for integration into Python- and R-based analysis workflows.
• Comprehensive CLI Tools: Provides command-line interface tools for common operations, including conversion between .hic and .mcool formats.
• C++ Core Library and Architecture: Uses a C++ core library with an architecture aimed at minimizing code duplication while maximizing flexibility.

Scientific Applications:

• Genome organization mapping: Processing Hi-C interaction matrices to support studies of three-dimensional genome architecture.
• Multi-resolution analysis: Handling interaction matrices at various resolutions to enable high-resolution genomic analyses.

Methodology:

Implements a C++ core library, provides command-line tools, and exposes Python and R bindings for operations including .hic ↔ .mcool conversion.