Honestly you are taking a big risk designing a DNA search algorithm something from scratch. It's akin to the risk people take when they roll their own crypto. There are aspects of this that you may not be considering, and it tends to be best to rest on the extensive work in the field than assume it is a trivial problem.
How do you deal with natural variation in the genome? Can you be sure your gRNA doesn't target an essential locus in some percentage people who carry a particular allele? The data to solve this is out there (1000 Genomes for instance).
Edit: excuse me, I appreciate that you are using a collection of whole genomes as your target. Will this reliably scale to thousands or millions of genomes and likely recombinations between them?
How do you deal with natural variation in the genome? Can you be sure your gRNA doesn't target an essential locus in some percentage people who carry a particular allele? The data to solve this is out there (1000 Genomes for instance).
Edit: excuse me, I appreciate that you are using a collection of whole genomes as your target. Will this reliably scale to thousands or millions of genomes and likely recombinations between them?