HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.

SALSA: A tool to scaffold long read assemblies with Hi-C data

A GAN-based method for Enhancing Hi-C data

C-Phasing/CPhasing: Phasing and scaffolding polyploid genomes based on Pore-C, HiFi-C/CiFi or Hi-C.

Nextflow DSL2 pipeline to generate a Genome Note, including assembly statistics, quality metrics, and Hi-C contact maps. This workflow is part of the Tree of Life production suite.

3DGB is a workflow to build 3D models of genomes from HiC data

Tools for processing HIC data.

FIREcaller: Python library for detecting Frequently Interacting REgions (FIREs) from Hi-C data

Snakemake pipeline for analysis and normalization of Hi-C data starting from fastq.gz files. It includes the possibility to perform grouped analyses, TAD, loops and stripes detections, as well as differential compartment and chromatin interaction analyses.

a Snakemake version of distiller - the Open2C Hi-C mapping workflow

Snakemake wrapper around the Arima Capture Hi-C (CHiC) workflow

A few tools for converting contact maps to .hic format compatible with the 4D Genome Browser.

Configurable Hi-C pipeline that is easy to use

A two-step model that combines neural network and ensemble learning to predict OCR–mediated interactions.

Snakemake workflow for processing Arima HIC data

A python library to display HiC data on a circular strip and to integrate genomic data

Hi-C Architect for Neural Networks

Make a phylogeny using the chromatin structure information extracted from Hi-C experiments (mirror of the original repo)

A GUI application for labeling HiC data with rectangles.