FORCAST

The Finding Optimizing and Reporting Cas Targets, or FORCAST pipeline enables researchers to design Cas-mediated mutagenesis experiments in model organisms with ease. Any Ensembl genome can be loaded and explored in the tool with the interactive genome browser JBrowse. Given a target sequence, potential guides can be generated using one of several possible RNA-guided endonulceases including Cas9, Cpf1/Cas12a, ScCas9, and others (custom RGENs are also possible). Guides are then evaluated for specificity by searching for potential off-targets with up to 4 mismatches across the genome of interest, scoring them, and assigning them a genetic context (intronic, exonic, intergenic).

Genotyping primers can be automatically designed for a set of guides using Primer3. Primers are evaluated for specificity using BLAST, and Silica. All oligonucleotides are visible in the genome browser as tracks and downloadable as doc, csv, or APE files. They are saved permanantly to the database and can be re-visited and exported at any point.

FORCAST provides a rigourous pipeline for genome editing and give you full control of your data. It's open source and completely free to use, modify, and install. Visit our GitHub for installation instructions.