multicrispr

multicrispr designs individual gRNAs and complex gRNA libraries for CRISPR/Cas9 and Prime Editing experiments through a genomic arithmetic framework that enables facile adaptation to recently introduced and future techniques.

Key Features:

• Genomic Target Definition and Transformation: Defines and transforms genomic targets using a genomic arithmetic framework.
• Spacer Finding: Identifies spacer sequences for gRNA design.
• Off-target Analysis: Counts offtarget (mis)matches to assess specificity.
• Targeting Efficiency Scoring: Computes Doench2016 and Doench2014 targeting efficiency scores.
• gRNA Detection, Scoring, and Filtering: Detects, scores, and filters gRNAs on both efficiency and specificity with target set-specific filtering.
• Visualization and Aggregation: Visualizes and aggregates results per target or CRISPR/Cas9 sequence.
• Output Generation: Returns both genomic ranges and sequences of gRNAs.
• Scalability: Scales well towards large target sets, enabling the design of large CRISPR/Cas9 libraries.

Scientific Applications:

• CRISPR/Cas9 Nucleotide Editing: Supports targeting the coding genome to introduce nucleotide deletions and insertions via CRISPR/Cas9 technology.
• Prime Editing: Provides gRNA design functionality for prime editing applications.
• APEX Proximity Labeling: Supports gRNA design for APEX proximity labeling methods.
• Homology Directed Repair: Facilitates gRNA design for homology directed repair approaches.
• Screening-like Approaches: Enables design of complex gRNA libraries for screening-like approaches requiring parallel targeting of thousands of targets.

Methodology:

The tool implements a genomic arithmetic framework as a computational basis for gRNA design, with functions to define and transform genomic targets, find spacers, count offtarget (mis)matches, and compute Doench2016/2014 targeting efficiency scores.