PT  - JOURNAL ARTICLE
AU  - Aaron McKenna
AU  - Jay Shendure
TI  - FlashFry: a fast and flexible tool for large-scale CRISPR target design
AID  - 10.1101/189068
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 189068
4099  - http://biorxiv.org/content/early/2017/09/14/189068.short
4100  - http://biorxiv.org/content/early/2017/09/14/189068.full
AB  - FlashFry is a fast and flexible command-line tool for characterizing large numbers of CRISPR target sequences. While several CRISPR web application exist, genome-wide knockout studies, noncoding deletion scans, and other large-scale studies or methods development projects require a simple and lightweight framework that can quickly discover and score thousands of candidates guides targeting an arbitrary DNA sequence. 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 widely used genome-wide sequence aligners, and output is provided as an easy-to-manipulate text file.Availability FlashFry is written in Scala and bundled as a stand-alone Jar file, easily run on any system with an installed Java virtual machine (JVM). The tool is freely licensed under version 3 of the GPL, and code, documentation, and tutorials are available on the GitHub page: http://aaronmck.github.io/FlashFry/