Fast and scalable off-target assessment for CRISPR guide RNAs using partial matches

The design of CRISPR-Cas9 guide RNAs requires the analysis of all potential target sites to determine the risk of unintentional edits for any given guide. A number of methods have been developed to evaluate this risk but the size of the target genome is a challenging factor. Many existing methods are limited by their need for an unfeasible amount of time or memory. In this paper, we introduce Crackling++, an update to our previous Crackling method, in which we have reduced processing time by imposing stricter matching criteria. We conducted a benchmark to compare our performance to other tools and show that Crackling++ is the fastest off-targeting scoring method and that it can scale to the largest genomes.