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.
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 |
- Code Repository (At GitHub, Track the package issue)
- PyPI (Download and Installation)
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