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.

Environment Variables¶

HPC_HICPRO_DIR - installation directory
HPC_HICPRO_BIN - executable directory

Categories¶

biology, pipeline, genomics