amplican

amplican analyzes amplicon sequencing data from genome editing experiments to quantify and visualize editing outcomes such as insertions, deletions, homology-directed repair (HDR), and targeted base editing.

Key Features:

• Nuclease-Optimized Alignments: Employs alignments optimized for nucleases to precisely map amplicon reads.
• Artifact Filtering: Filters experimental artifacts to focus analysis on genuine genome editing events.
• Event-Specific Normalization: Applies normalization tailored to each type of editing event for accurate quantification.
• Off-Target Read Detection: Detects off-target reads to identify unintended genomic modifications.
• Quantification of Genome Editing Events: Quantifies insertions, deletions, homology-directed repair (HDR), and targeted base editing from amplicon reads.
• Visualization of Genome Editing Events: Generates visual representations of editing outcomes to aid interpretation.
• Scalability: Scales to thousands of amplicon sequencing-based experiments and is applicable to CRISPR studies.
• Automated Control Integration: Automates integration of controls within the analysis pipeline to account for biases.

Scientific Applications:

• CRISPR editing evaluation: Assess efficiency and specificity of CRISPR genome editing experiments.
• Off-target assessment: Identify and quantify unintended genomic modifications detected among amplicon reads.
• Editing outcome quantification: Measure frequencies of insertions, deletions, HDR, and targeted base editing across samples.
• Amplicon sequencing studies: Analyze large-scale amplicon sequencing datasets for genome editing research.

Methodology:

Aligns amplicon reads using nuclease-optimized algorithms, filters experimental artifacts, applies event-specific normalization, detects off-target reads, integrates controls, and quantifies and visualizes genome editing events.