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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.

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    $\begingroup$ I don't have enough experience with CRISPR to give a useful answer. I have one observation though. You say that you are afraid that CRISPRseek might be quite slow for a genome-scale search. Have you actually tried? It sounds like this problem should parallelize well. Presumably, you could run one gene at a time, running as many in parallel as your resources allow? $\endgroup$ May 25 '17 at 22:18
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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.

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