H!
Which bioinformatics tools supporting CRISPR-Cas Experiments do you recommend? Or which tools are you using?

Hi
You can try our package in R, [Casilico][1]. It supports  Cas12, Cas13, and Cas14 CRISPR-Cas systems. Using a list of important features such as mismatch tolerance rules, self-complementarity, GC content, frequency of cleaving base around the target site, target accessibility and PFS (protospacer flanking site) or PAM (protospacer adjacent motif) requirement, CaSilico searches all potential crRNAs in a user-input sequence. 

CaSilico outperforms previous crRNA design tools in the following respects: 1) supporting any reference genome/transcriptome for which a FASTA file is available; 2) designing crRNAs that simultaneously target multiple sequences through conserved region detection among a set of sequences; 3) considering new CRISPR-Cas subtypes; 4) reporting a list of different features for each candidate crRNA, which can help the user to select the best one. Our paper was puplished in [Frontiers in Bioengineering and Biotechnology][2]. ![enter image description here][3]

Our tool is sufficiently flexible to tune some key parameters governing the design of crRNA and identification of off-targets, which can be led to increases the chances of successful CRISPR-Cas experiments. Given these capabilities, Casilico addresses end-user concerns arising from the use of sophisticated bioinformatics algorithms and has a wide range of potential research applications in different areas especially design of crRNA for pathogen diagnosis. Casilico was successfully applied to design crRNAs for different genes in SARS-CoV-2 genome, as some of the crRNAs have been experimentally tested in the previous studies.


  [1]: https://github.com/mrb20045/CaSilico
  [2]: https://www.frontiersin.org/articles/10.3389/fbioe.2022.957131/full
  [3]: https://user-images.githubusercontent.com/9910942/158050606-9c592f1c-c0a4-4a4e-8cf8-ded8e0c7e7b6.png