Genome-wide CRISPR guide RNA design and specificity analysis with GuideScan2
Henri Schmidt, Minsi Zhang, Dimitar Chakarov, Vineet Bansal, Haralambos Mourelatos, Francisco J. Sánchez‐Rivera, Scott W. Lowe, Andrea Ventura, Christina S. Leslie, Yuri Pritykin
Abstract
We present GuideScan2 for memory-efficient, parallelizable construction of high-specificity CRISPR guide RNA (gRNA) databases and user-friendly design and analysis of individual gRNAs and gRNA libraries for targeting coding and non-coding regions in custom genomes. GuideScan2 analysis identifies widespread confounding effects of low-specificity gRNAs in published CRISPR screens and enables construction of a gRNA library that reduces off-target effects in a gene essentiality screen. GuideScan2 also enables the design and experimental validation of allele-specific gRNAs in a hybrid mouse genome. GuideScan2 will facilitate CRISPR experiments across a wide range of applications.