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FlashFry: a fast and flexible tool for large-scale CRISPR target design

BMC Biol. 2018 Jul 5;16(1):74. doi: 10.1186/s12915-018-0545-0.

Abstract

Background: Genome-wide knockout studies, noncoding deletion scans, and other large-scale studies require a simple and lightweight framework that can quickly discover and score thousands of candidate CRISPR guides targeting an arbitrary DNA sequence. While several CRISPR web applications exist, there is a need for a high-throughput tool to rapidly discover and process hundreds of thousands of CRISPR targets.

Results: Here, we introduce FlashFry, a fast and flexible command-line tool for characterizing large numbers of CRISPR target sequences. With FlashFry, users can specify an unconstrained number of mismatches to putative off-targets, richly annotate discovered sites, and tag potential guides with commonly used on-target and off-target scoring metrics. FlashFry runs at speeds comparable to commonly used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file.

Conclusions: FlashFry is a fast and convenient command-line tool to discover and score CRISPR targets within large DNA sequences.

Keywords: CRISPR; Cas9; Cpf1; Deletion scan; Guide library; Off-target; On-target.

Publication types

  • Evaluation Study
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Base Sequence
  • Clustered Regularly Interspaced Short Palindromic Repeats*
  • Databases, Genetic
  • Gene Editing*
  • Genome
  • Sequence Analysis, DNA / methods*
  • Software*