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

作者：Aaron McKenna, Jay Shendure · 发表于：BMC Biology · 年份：2018 · DOI：10.1186/s12915-018-0545-0 · 被引用次数：178 · 研究领域：CRISPR and Genetic Engineering、Single-cell and spatial transcriptomics、Biotechnology and Related Fields

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.