HiC-Pro

Description

HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to normalized contact maps. It supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzymes such as DNase Hi-C. In practice, HiC-Pro was successfully applied to many data-sets including dilution Hi-C, in situ Hi-C, DNase Hi-C, Micro-C, capture-C, capture Hi-C or HiChip data.

The pipeline is flexible, scalable and optimized. It can operate either on a single laptop or on a computational cluster. HiC-Pro is sequential and each step of the workflow can be run independantly. HiC-Pro includes a fast implementatation of the iterative correction method (see the iced python package for more information). Finally, HiC-Pro can use phasing data to build allele-specific contact maps.

Environment Modules

Run module spider HiC-Pro to find out what environment modules are available for this application.

System Variables

HPC_HIC-PRO_DIR - installation directory
HPC_HIC-PRO_BIN - executable directory

Additional Information

Obtain an editable configuration file template by issuing the following command from your project directory:

 cp ${HPC_HICPRO_DIR}/config-hicpro.txt /path/to/your/project/

Help on setting up the configuration file: https://github.com/nservant/HiC-Pro/blob/master/doc/MANUAL.md#setting-the-configuration-file

Citation

If you publish research that uses HiC-Pro you have to cite it as follows:

Servant N., Varoquaux N., Lajoie BR., Viara E., Chen CJ., Vert JP., Dekker J., Heard E., Barillot E. HiC-Pro: An optimized and flexible pipeline for Hi-C processing. Genome Biology 2015, 16:259 doi:10.1186/s13059-015-0831-x