hictkpy

hictkpy provides Python bindings for the hictk C++ library to read and write .hic and Cooler (.cool/.mcool) Hi-C contact map files for manipulation of interaction matrices and study of genome organization.

Key Features:

• Transparent file handling: Native support for .hic and Cooler (.cool and .mcool) binary formats for Hi-C interaction matrices.
• High performance: C++ implementation with Python bindings for optimized performance, with benchmarking indicating advantages over existing tools.
• Cross-language bindings: Provides R bindings in addition to Python bindings for multi-language integration.
• Format conversion: Supports conversion between .hic and .mcool file formats.

Scientific Applications:

• Genome organization mapping: Processing Hi-C contact maps to study three-dimensional genome organization.
• Comparative Hi-C analyses: Enabling comparative studies across datasets stored in .hic and Cooler formats without intermediate reformatting.
• Custom pipeline development: Integrating .hic and .cool/.mcool data into bespoke analysis pipelines.

Methodology:

Implemented as a C++ library with Python and R bindings that reads and writes .hic and Cooler (.cool/.mcool) files and supports conversion between .hic and .mcool.