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 0.8.1, runHiC can be used directly on Arima HiC data by setting the enzyme name to Arima.
runHiC is designed to process Hi-C data from raw sequencing reads(.sra, .fastq, .fastq.gz) to the ICE-corrected contact matrices. It currently contains 5 subcommand:
|mapping||Map raw pair-end sequencing data to a supplied genome. Support three read aligners: chromap, bwa and minimap2.|
|filtering||Perform read-level and fragment-level noise removing|
|binning||1.Generate contact matirx; 2. Perform ICE/matrix-balancing normalization|
|pileup||Perform entire processing from mapping to binning|
|quality||Assess the quality of your Hi-C data|
Open a terminal, type runHiC -h or 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
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