JACKIE: Fast enumeration of single- and multi-copy CRISPR binding sites

Summary: CRISPR-based methods for genome, epigenome editing and imaging have provided powerful tools to interrogate the functions of the genome. The design of guide RNA (gRNA) is a vital step of CRISPR experiments. We report here the implementation of JACKIE (Jackie and Albert9s CRISPR K-mer Instances Enumerator), a pipeline for enumerating all potential single- and multi-copy CRISPR sites in the genome. We demonstrate the application of JACKIE to identify locus-specific repetitive sequences for CRISPR/Casilio-based genomic labeling. Availability: Source codes and CRISPR site databases (JACKIEdb) for hg38 and mm10 are available for download at http://crispr.software/JACKIE