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

Bioinformatics. 2019 Sep 1;35(17):3146-3147. doi: 10.1093/bioinformatics/btz019.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • CRISPR-Cas Systems
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Gene Editing
  • Genome*
  • RNA, Guide, CRISPR-Cas Systems
  • Software

Substances

  • RNA, Guide, CRISPR-Cas Systems