In silico simulation of high-throughput sequencing data is a technique used widely in the genomics field. However, there is currently a lack of effective tools for creating simulated data from nanopore sequencing devices, which measure DNA or RNA molecules in the form of time-series current signal data. Here, we introduce Squigulator, a fast and simple tool for simulation of realistic nanopore signal data. Squigulator takes a reference genome, a transcriptome, or read sequences, and generates corresponding raw nanopore signal data. This is compatible with basecalling software from Oxford Nanopore Technologies (ONT) and other third-party tools, thereby providing a useful substrate for development, testing, debugging, validation, and optimization at every stage of a nanopore analysis workflow. The user may generate data with preset parameters emulating specific ONT protocols or noise-free “ideal” data, or they may deterministically modify a range of experimental variables and/or noise parameters to shape the data to their needs. We present a brief example of Squigulator's use, creating simulated data to model the degree to which different parameters impact the accuracy of ONT basecalling and downstream variant detection. This analysis reveals new insights into the nature of ONT data and basecalling algorithms. We provide Squigulator as an open-source tool for the nanopore community.

中文翻译：

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具有可调参数的纳米孔测序信号数据模拟


高通量测序数据的计算机模拟是基因组学领域广泛使用的一项技术。然而，目前缺乏有效的工具来从纳米孔测序设备创建模拟数据，纳米孔测序设备以时间序列电流信号数据的形式测量 DNA 或 RNA 分子。在这里，我们介绍 Squigulator，这是一种快速、简单的工具，用于模拟真实的纳米孔信号数据。 Squigulator 采用参考基因​​组、转录组或读取序列，并生成相应的原始纳米孔信号数据。它与 Oxford Nanopore Technologies (ONT) 的碱基识别软件和其他第三方工具兼容，从而为纳米孔分析工作流程每个阶段的开发、测试、调试、验证和优化提供有用的底物。用户可以使用模拟特定ONT协议的预设参数或无噪声“理想”数据来生成数据，或者他们可以确定性地修改一系列实验变量和/或噪声参数以根据他们的需要调整数据。我们提供了 Squigulator 使用的一个简短示例，创建模拟数据来模拟不同参数影响 ONT 碱基识别和下游变异检测准确性的程度。该分析揭示了对 ONT 数据和碱基识别算法本质的新见解。我们为纳米孔社区提供 Squigulator 作为开源工具。