Coolsecture: an easy-to-use and improved framework for cross-species Hi-C contact map comparison

SUMMARY: Cross-species Hi-C comparison remains challenging because existing workflows often rely on multiple scripts, heterogeneous I/O formats, and limited diagnostic support. We present coolsecture, a Python 3 command-line toolkit that integrates multiple contact-matrix and synteny formats with bidirectional lift-over and reciprocal consistency assessment, multi-resolution percentile-based comparison, diagnostic visualization, and cross-sample similarity analysis, providing a streamlined and reproducible framework for comparative Hi-C analysis. AVAILABILITY AND IMPLEMENTATION: coolsecture is distributed under the GPL-3 license. Source code, Snakemake workflows, and documentation are freely available at https://github.com/pk-zhu/Coolsecture and are archived on Figshare at https://doi.org/10.6084/m9.figshare.30158440.