RT Journal Article
SR Electronic
T1 FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 2020.04.21.053090
DO 10.1101/2020.04.21.053090
A1 Hillary Elrick
A1 Viswateja Nelakuditi
A1 Greg Clark
A1 Michael Brudno
A1 Arun K. Ramani
A1 Lauryl M.J. Nutter
YR 2020
UL http://biorxiv.org/content/early/2020/04/23/2020.04.21.053090.abstract
AB Cas-mediated genome editing has enabled researchers to perform mutagenesis experiments with relative ease. Effective genome editing requires tools for guide RNA selection, off-target prediction, and genotyping assay design. While independent tools exist for these functions, there is still a need for a comprehensive platform to design, view, evaluate, store, and catalogue guides and their associated primers. The Finding Optimizing and Reporting Cas Targets (FORCAST) application integrates existing open source tools such as JBrowse, Primer3, BLAST, bwa, and Silica to create a complete allele design and quality assurance pipeline. FORCAST is a fully integrated software that allows researchers performing Cas-mediated genome editing to generate, visualize, store, and share information related to guides and their associated experimental parameters. It is available from a public GitHub repository and as a Docker image, for ease of installation and portability.Competing Interest StatementThe authors have declared no competing interest.