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bioRxiv · 10.1101/2021.06.28.450164

GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes

Poudel, R.·Trujillo Rodriguez, L.·Reisch, C. R.·Rivers, A. R.
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Abstract

BackgroundCRISPR-Cas systems have expanded the possibilities for gene editing in bacteria and eukaryotes. There are many excellent tools for designing the CRISPR-Cas guide RNAs for model organisms with standard Cas enzymes. GuideMaker is intended as a fast and easy-to-use design tool for atypical projects with 1) non-standard Cas enzymes, 2) non-model organisms, or 3) projects that need to design a panel of guide RNAs (gRNA) for genome-wide screens. FindingsGuideMaker can rapidly design gRNAs for gene targets across the genome from a degenerate protospacer adjacent motif (PAM) and a GenBank file. The tool applies Hierarchical Navigable Small World (HNSW) graphs to speed up the comparison of guide RNAs. This allows the user to design gRNAs targeting all genes in a typical bacterial genome in about 1-2 minutes. ConclusionsGuidemaker enables the rapid design of genome-wide gRNA for any CRISPR-Cas enzyme in non-model organisms. While GuideMaker is designed with prokaryotic genomes in mind, it can efficiently process smaller eukaryotic genomes as well. GuideMaker is available as command-line software, a stand-alone web application, and a tool in the CyCverse Discovery Environment. All versions are available under a Creative Commons CC0 1.0 Universal Public Domain Dedication.

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Poudel, R., Trujillo Rodriguez, L., Reisch, C. R., Rivers, A. R.. 2021-06-29. GuideMaker: Software to design CRISPR-Cas guide RNA pools in non-model genomes. https://doi.org/10.1101/2021.06.28.450164

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