runHiC 0.7.0-r2

A easy-to-use Hi-C processing software based on hiclib

runHiC is a easy-to-use Hi-C processing software based on hiclib (https://bitbucket.org/mirnylab/hiclib) Different from hiclib, which was born for flexibility, runHiC is a customized pipeline, and can be run from command line directly.

Since version 0.7.0, runHiC has been able to execute concurrently either on a single laptop with multiple processors or on a PBS-based clusters.

Design Concepts

runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the corrected contact matrices. It separates the whole procedure into 4 stages(mapping, filtering, binning, correcting) and contains 7 subcommands:

mapping	Iteratively map pair-end sequencing reads to a supplied genome
filtering	Perform read-level and fragment-level noise removing
binning	Generate the original contact matrices
correcting	Perform iterative corrections on original contact matrices
tosparse	Convert the dense intra-chromosomal contact matrices to sparse ones
pileup	Streamline all stages from mapping to correcting
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