SIQ

SIQ analyzes targeted Sanger and next-generation sequencing data (Illumina short reads and PacBio long reads) to identify and quantify deletions, single-nucleotide variations, templated insertions, and tandem duplications resulting from CRISPR-mediated genome editing.

Key Features:

• Versatile Data Processing: Processes targeted Sanger sequences and a range of NGS data, explicitly including Illumina short reads and PacBio long reads.
• Comprehensive Mutation Profiling: Classifies and quantifies genomic events including deletions, single-nucleotide variations (SNVs), templated insertions, and tandem duplications.
• Visualization with SIQPlotteR: Outputs results for interactive visualization via SIQPlotteR, including tornado plot visualizations of mutational signatures.

Scientific Applications:

• CRISPR-mediated genome editing: Identifies sequence- and repair pathway-specific mutational signatures and quantifies editing outcomes from CRISPR experiments.
• Cross-species targeted sequencing: Enables analysis of targeted sequencing datasets from model systems such as nematodes, plants, and mammalian cell cultures.

Methodology:

SIQ retrieves relevant sequencing datasets and applies algorithms to classify and quantify mutational events; integration with SIQPlotteR enables direct visualization of the resulting mutational profiles.