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Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.

ABSTRACT: SUMMARY:CRISPR/Cas9 system requires short guide RNAs (sgRNAs) to direct genome modification. Most currently available tools for sgRNA design operate only with standard reference genomes, and are best suited for small-scale projects. To address these limitations, we developed Crisflash, a software tool for fast sgRNA design and potential off-target discovery, built for performance and flexibility. Crisflash can rapidly design CRISPR guides against any sequenced genome or genome sequences, and can optimize guide accuracy by incorporating user-supplied variant data. Crisflash is over an order of magnitude faster than comparable tools, even using a single CPU core, and efficiently and robustly scores the potential off-targeting of all possible candidate CRISPR guide oligonucleotides. AVAILABILITY AND IMPLEMENTATION:https://github.com/crisflash. SUPPLEMENTARY INFORMATION:Supplementary data are available at Bioinformatics online.

SUBMITTER: Jacquin ALS 

PROVIDER: S-EPMC6735888 | biostudies-other | 2019 Sep

REPOSITORIES: biostudies-other

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Crisflash: open-source software to generate CRISPR guide RNAs against genomes annotated with individual variation.

Jacquin Adrien L S ALS   Odom Duncan T DT   Lukk Margus M  

Bioinformatics (Oxford, England) 20190901 17

<h4>Summary</h4>CRISPR/Cas9 system requires short guide RNAs (sgRNAs) to direct genome modification. Most currently available tools for sgRNA design operate only with standard reference genomes, and are best suited for small-scale projects. To address these limitations, we developed Crisflash, a software tool for fast sgRNA design and potential off-target discovery, built for performance and flexibility. Crisflash can rapidly design CRISPR guides against any sequenced genome or genome sequences,  ...[more]