runHiC 0.8.0

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

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

Links

• Detailed Documentation

  • Installation

  • Quick Start

  • Data Quality

  • Parallel Computation

• Code Repository (At GitHub, Track the package issue)

• PyPI (Download and Installation)

Usage

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

Citation

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