Biowulf High Performance Computing at the NIH
CutRunTools: a flexible pipeline for CUT&RUN processing and footprint analysis

CutRunTools is a pipeline for analysis of data produced by the CUT&RUN (Cleavage Under Targets and Release Using Nuclease) technology for high-resolution mapping of DNA binding sites. It is a flexible, general pipeline that facilitates identification of chromatin-associated protein binding and performs genomic footprinting analysis from antibody-targeted CutRun primary cleavage data. CutRunTools extracts endonuclease cut site information from sequences of short read fragments and produces single-locus binding estimates, aggregate motif footprints, and informative visualizations to support the high-resolution mapping capability of CutRun