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Last pushed: 2 years ago
Short Description
HiC-Pro process Hi-C data, from fastq (paired-end Illumina data) to the normalized contact maps.
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What is HiC-Pro ?
HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro can analyse data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C.
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 ICE normalization method (see the iced python library for more information).

If you use HiC-Pro, please cite :

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

For any question about HiC-Pro, please contact or use the HiC-Pro forum !

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