SIQ: easy quantitative measurement of mutation profiles in sequencing data
Robin van Schendel1, Joost Schimmel1, Marcel Tijsterman1,2
1Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
NAR Genomics and Bioinformatics
|September 8, 2022
Summary
Sequence Interrogation and Quantification (SIQ) is a new software tool for analyzing genome editing outcomes. It helps researchers easily visualize and interpret complex sequencing data, revealing mutational signatures across different model systems.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- CRISPR-mediated genome editing necessitates efficient analysis of diverse outcomes.
- Existing tools may not adequately process or visualize complex targeted sequencing data.
Purpose of the Study:
- To introduce Sequence Interrogation and Quantification (SIQ), a user-friendly software for analyzing genome editing results.
- To enable data mining and visualization of targeted sequencing data, including next-generation sequencing (NGS).
Main Methods:
- Development of SIQ software for processing Sanger and next-generation sequencing (NGS) data (Illumina, PacBio).
- Implementation of mutational profile analysis with classification of events (deletions, SNVs, insertions, duplications).
- Integration with SIQPlotteR, an interactive web tool for data visualization using tornado plots.
Main Results:
- SIQ effectively processes and visualizes complex targeted sequencing data.
- The tool establishes mutational profiles, classifying various genetic alterations.
- SIQPlotteR provides insightful tornado plots for clear data interpretation.
Conclusions:
- SIQ offers a simple yet powerful solution for analyzing genome editing outcomes.
- The software facilitates the identification of sequence- and repair pathway-specific mutational signatures.
- SIQ is applicable across diverse model systems, including nematodes, plants, and mammalian cell cultures.
