Skip to main content

A easy-to-use Hi-C processing software supporting distributed computation

Project description

runHiC is an easy-to-use command-line tool for Hi-C data processing.

Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to Pairs and Cooler, to comply with 4DN standards. (See Release Notes)

Design Concepts

runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the corrected contact matrices. It currently contains 5 subcommand:

mapping Map raw pair-end sequencing data to a supplied genome. Support bwa and minimap2.
filtering Perform read-level and fragment-level noise removing
binning 1.Generate contact matirx; 2. Perform ICE
pileup Perform entire processing from mapping to binning
quality Assess the quality of your Hi-C data


Open a terminal, type runHiC -h and runHiC <subcommand> -h for help information.


Xiaotao Wang. (2016). runHiC: A user-friendly Hi-C data processing software based on hiclib. Zenodo. 10.5281/zenodo.55324

Project details

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Filename, size & hash SHA256 hash help File type Python version Upload date
runHiC-0.8.0.post3-py3-none-any.whl (20.1 kB) Copy SHA256 hash SHA256 Wheel py3
runHiC-0.8.0.post3.tar.gz (31.2 kB) Copy SHA256 hash SHA256 Source None

Supported by

Elastic Elastic Search Pingdom Pingdom Monitoring Google Google BigQuery Sentry Sentry Error logging AWS AWS Cloud computing DataDog DataDog Monitoring Fastly Fastly CDN SignalFx SignalFx Supporter DigiCert DigiCert EV certificate StatusPage StatusPage Status page