Yanpeng talked to me last week and mentioned that he hopes I could write a script to help design gRNA selection in wheat. There is one website, CRISPR-P 2.0, for designing gRNAs in plants, but it does not include wheat. Beyond that, wheat is a hexaploid wheat and usually, we want to design gRNAs that can target all 3 homeologs in wheat’s A, B, D genomes. So even the wheat genome is publicly available, the CRISPR-P 2.0 may still need some big update to handle polyploid species.
The script is now finished, and it is called CRISPR-wheat, which is available in my github. I used the same software, BatMis, to find potential mismatches in the wheat genome. After working on CRISPR sgRNAs for a while, I think you can just use CRISPR-P 2.0 if they included wheat genome. The website does not need to update others, because they can use the gene on one of the A, B, D genome of wheat to find sgRNAs, and then you can check the hits on the genome to know whether they hit the other two sub-genomes.
More details of CRISPR-wheat is in the README. I also listed detailed steps on how to prepare all the needed files. Hope it helps.