iGUIDE

iGUIDE refines detection and quantification of on-target and off-target CRISPR-Cas9 cleavage sites and characterizes associated deletions to improve cleavage specificity analysis.

Key Features:

• Mispriming Event Filtering: Implements algorithmic filtering to remove mispriming-derived noise that can obscure true double-strand break (DSB) signals.
• Comprehensive Cleavage Site Mapping: Precisely specifies genomic locations of Cas9-guided cleavages across multiple guide RNAs.
• Deletion Characterization: Identifies and characterizes deletions associated with CRISPR-induced cleavage events.
• Background DSB Association Analysis: Associates naturally occurring background DSBs with genomic features such as open chromatin, high gene density, and chromosomal fragile sites.

Scientific Applications:

• Off-target assessment in genome editing: Enables accurate mapping and quantification of CRISPR-Cas9 off-target cleavage sites for evaluating editing specificity.
• Characterization of induced genomic alterations: Supports analysis of deletions and other sequence alterations resulting from CRISPR activity.
• Distinguishing CRISPR-induced versus natural DSBs: Facilitates separation of nuclease-induced breaks from background DSBs by relating breaks to chromatin state and genomic context.

Methodology:

Computational pipeline that improves upon GUIDE-seq by incorporating algorithms to filter mispriming noise and thereby refine detection, quantification, and deletion characterization of CRISPR-Cas9 cleavage sites.