SIQ: easy quantitative measurement of mutation profiles in sequencing data

Robin van Schendel; Joost Schimmel; Marcel Tijsterman

doi:10.1093/nargab/lqac063

SIQ: easy quantitative measurement of mutation profiles in sequencing data

NAR Genom Bioinform. 2022 Sep 5;4(3):lqac063. doi: 10.1093/nargab/lqac063. eCollection 2022 Sep.

Authors

Robin van Schendel¹, Joost Schimmel¹, Marcel Tijsterman^{1

2}

Affiliations

¹ Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
² Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.

Abstract

With the emergence of CRISPR-mediated genome editing, there is an increasing desire for easy-to-use tools that can process and overview the spectra of outcomes. Here, we present Sequence Interrogation and Quantification (SIQ), a simple-to-use software tool that enables researchers to retrieve, data-mine and visualize complex sets of targeted sequencing data. SIQ can analyse Sanger sequences but specifically benefit the processing of short- and long-read next-generation sequencing data (e.g. Illumina and PacBio). SIQ facilitates their interpretation by establishing mutational profiles, with a focus on event classification such as deletions, single-nucleotide variations, (templated) insertions and tandem duplications. SIQ results can be directly analysed and visualized via SIQPlotteR, an interactive web tool that we made freely available. Using insightful tornado plot visualizations as outputs, we illustrate that SIQ readily identifies sequence- and repair pathway-specific mutational signatures in a variety of model systems, such as nematodes, plants and mammalian cell culture.