Next-generation sequencing (NGS)-library preparation for whole-genome sequencing (WGS) starts with DNA fragmentation, and sonication is a physical approach used most often due to its simplicity and reproducibility. However, the commercially available Covaris instrument has a high price for both the device and consumables. Here, we describe our in-house method of DNA shearing by sonication with small (100–600 µm) glass beads and an ultrasonic bath. The fragmentation conditions were optimized for the bacterial WGS with ∼550-bp fragment size (the ultrasonic bath water temperature 5–10°C, glass beads 0.06 g, the fragmentation time 50 s) and for human DNA with ∼250 bp (fragmentation with the same parameters for 4 min). Fragmentation results were compared with the Covaris instrument for preparing several bacterial NGS libraries for Illumina NGS platforms by several characteristics. We obtained close mean fragment lengths (523–623 versus 480–646), similar mono- and dinucleotide specificity of shearing, and comparable indicators of read alignment and de novo assembly for both methods. Thus, the described method is a new fast, and effective DNA fragmentation approach that can be used in different WGS applications.

中文翻译：

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一种廉价、简单且有效的 NGS 文库基因组 DNA 片段化方法

用于全基因组测序 (WGS) 的新一代测序 (NGS) 文库制备始于 DNA 片段化，而超声处理因其简单性和可重复性而成为最常用的物理方法。然而，市售的 Covaris 仪器的设备和耗材价格都很高。在这里，我们描述了我们内部的 DNA 剪切方法，该方法使用小 (100–600 µm) 玻璃珠和超声波浴进行超声处理。对片段大小约为 550 bp 的细菌 WGS（超声波浴水温 5-10°C，玻璃珠 0.06 g，片段化时间 50 s）和大约 250 bp 的人类 DNA（用相同的参数 4 分钟）。将片段化结果与 Covaris 仪器进行比较，通过几个特征为 Illumina NGS 平台准备几个细菌 NGS 文库。我们获得了接近的平均片段长度（523-623 对 480-646），相似的剪切单核苷酸和二核苷酸特异性，以及两种方法的读取对齐和从头组装的可比指标。因此，所描述的方法是一种新的快速、有效的 DNA 片段化方法，可用于不同的 WGS 应用。