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FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments

View ORCID ProfileHillary Elrick, View ORCID ProfileViswateja Nelakuditi, Greg Clark, Michael Brudno, Arun K. Ramani, View ORCID ProfileLauryl M.J. Nutter
doi: https://doi.org/10.1101/2020.04.21.053090
Hillary Elrick
1Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
2The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
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  • ORCID record for Hillary Elrick
Viswateja Nelakuditi
1Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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Greg Clark
2The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
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Michael Brudno
1Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
3Department of Computer Science, University of Toronto, Toronto, ON M5T 3A1, Canada
4University Health Network, Toronto, ON, Canada
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Arun K. Ramani
1Centre for Computational Medicine, The Hospital for Sick Children, Toronto, ON M5G 1X8, Canada
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  • For correspondence: lauryl.nutter@sickkids.ca
Lauryl M.J. Nutter
2The Centre for Phenogenomics, The Hospital for Sick Children, Toronto, ON M5T 3H7, Canada
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  • ORCID record for Lauryl M.J. Nutter
  • For correspondence: lauryl.nutter@sickkids.ca
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Abstract

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 Statement

The authors have declared no competing interest.

Footnotes

  • https://github.com/ccmbioinfo/FORCAST

  • https://ccmbioinfo.github.io/FORCAST/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted April 23, 2020.
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FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments
Hillary Elrick, Viswateja Nelakuditi, Greg Clark, Michael Brudno, Arun K. Ramani, Lauryl M.J. Nutter
bioRxiv 2020.04.21.053090; doi: https://doi.org/10.1101/2020.04.21.053090
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FORCAST: a fully integrated and open source pipeline to design Cas-mediated mutagenesis experiments
Hillary Elrick, Viswateja Nelakuditi, Greg Clark, Michael Brudno, Arun K. Ramani, Lauryl M.J. Nutter
bioRxiv 2020.04.21.053090; doi: https://doi.org/10.1101/2020.04.21.053090

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