van Schendel Robin, Schimmel Joost, Tijsterman Marcel
Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
Institute of Biology Leiden, Leiden University, Leiden, The Netherlands.
NAR Genom Bioinform. 2022 Sep 5;4(3):lqac063. doi: 10.1093/nargab/lqac063. eCollection 2022 Sep.
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.
随着CRISPR介导的基因组编辑技术的出现，人们对能够处理和概述结果谱的易用工具的需求日益增加。在此，我们展示了序列询问与定量（SIQ），这是一种易于使用的软件工具，使研究人员能够检索、挖掘数据并可视化复杂的靶向测序数据集。SIQ可以分析桑格测序数据，但特别有利于处理短读长和长读长的下一代测序数据（如Illumina和PacBio）。SIQ通过建立突变谱促进对这些数据的解读，重点关注事件分类，如缺失、单核苷酸变异、（模板化）插入和串联重复。SIQ结果可以通过SIQPlotteR直接进行分析和可视化，SIQPlotteR是我们免费提供的一个交互式网络工具。通过使用有洞察力的龙卷风图可视化作为输出，我们表明SIQ能够在多种模型系统中轻松识别序列和修复途径特异性的突变特征，如线虫、植物和哺乳动物细胞培养。
