CustardPy is a 3D genome analysis tool written in Python3 and available using the Docker system. It is mainly designed for multi-sample Hi-C analysis (e.g., comparison of depletion effects across multiple proteins) and provides various functions for analysis and visualization.

Since the docker image includes various existing tools in addition to the core CustardPy component (see Installation), users can perform a variety of 3D genome analyses without having to install them individually.

  • Major Release! (version 1)
    • Unified the Docker images for CustardPy and CustardPy_Juicer. Version 1 of the CustardPy docker image now supports all analyses previously offered by CustardPy and CustardPy_Juicer, rendering the latter unnecessary.


Fig. 1 The workflow of CustardPy for a single sample (A), two samples (B) and multiple sample comparison (C).



  • Nakato R, Sakata T, Wang J, Nagai LAE, Nagaoka Y, Oba GM, Bando M, Shirahige K, Context-dependent perturbations in chromatin folding and the transcriptome by cohesin and related factors, Nature Communications, 2023. doi: 10.1038/s41467-023-41316-4