Large-scale gRNA design for a CRISPR screen What are the best tools to design gRNAs in a high-throughput way for a CRISPR screen, e.g. targeting all protein-coding genes in a genome? I would like to take into account possible off-target effects, as well as to allow for flexibility in the PAM sequence, to have the possibility of using non-canonical PAMs.

I'm aware of CRISPRseek, but I'm afraid it might be quite slow to run for a genome-scale search.
Perhaps GenomeCRISPR, I've personally never used it, but it has a well-documented API and appears you could automate it to go through the whole genome.