hichipper: a preprocessing pipeline for calling DNA loops from HiChIP data

Mumbach et al. recently described HiChIP, a novel protein-mediated chromatin conformation assay that lowers cellular input requirements while simultaneously increasing the yield of informative reads compared to previous methods. To facilitate the dissemination and adoption of this assay, we introduce hichipper (http://aryeelab.org/hichipper), an open-source HiChIP data preprocessing tool, with features that include bias-corrected peak calling, library quality control, DNA loop calling, and output of processed data for downstream analysis and visualization.