JACKIE: Fast enumeration of genomic single- and multi-copy target sites and their off-targets for CRISPR and other engineered nuclease systems

ZFP-, TALE-, and CRISPR-based methods for genome, epigenome editing and imaging have provided powerful tools to interrogate functions of genomes. Targeting sequence design is vital to the success of these experiments. While existing design software mainly focus on designing target sequence for specific elements, we report here the implementation of JACKIE (Jackie and Alberts Comprehensive K-mer Instances Enumerator), a suite of software for enumerating all single- and multi-copy sites in the genome that can be incorporated for genome-scale designs as well as loaded onto genome browsers alongside other tracks for convenient web-based graphic-user-interface (GUI)-enabled design. We also implement fast algorithms to identify sequence neighborhoods or off-target counts of targeting sequences so that designs with low probability of off-target can be identified among millions of design sequences in reasonable time. We demonstrate the application of JACKIE-designed CRISPR site clusters for genome imaging.