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.

• Repository
• PyPI

Please check the file "INSTALL.rst" in the distribution.

runHiC is able to perform the entire analysis from sequencing data to corrected contact matrices. It separates the whole process into 4 stages(mapping, filtering, binning, correcting).

7 subcommands are available:

Please refer to the Sample folder distributed with our source code.

Although not required, I recommend creating a data root directory separate from the working directory.

Both genome and sequencing data should be placed under the data root directory.

Genome sequences should be stored chromosome by chromosome in FASTA format under a subfolder(named after corresponding genome name).

Sequencing read-pairs should be stored in SRA or FASTQ format under another subfolder(any valid name).

Construct a meta data file describing your sequencing data under the working directory

Four columns are required: prefix of SRA file name, cell line name, biological replicate label, and restriction enzyme name. An example file(Sample/working/datasets.tsv) is distributed along with this software, please check it.

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