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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 versio 0.8.5, runHiC has changed the default aligner to chromap, which is comparable to bwa-mem in alignment accuracy, but runs over 10 times faster.

Since version 0.8.1, runHiC can be used directly on Arima HiC data by setting the enzyme name to Arima.

Since version 0.8.0, runHiC has changed its default data container/format from HDF5 to Pairs and Cooler.

Design Concepts

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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