Next generation sequencing is in the process of evolving from a technology used for research purposes to one which is applied in clinical diagnostics. Recently introduced high throughput and benchtop instruments offer fully automated sequencing runs at a lower cost per base and faster assay times. In turn, the complex and cumbersome library preparation, starting with isolated nucleic acids and resulting in amplified and barcoded DNA with sequencing adapters, has been identified as a significant bottleneck. Library preparation protocols usually consist of a multistep process and require costly reagents and substantial hands-on-time. Considerable emphasis will need to be placed on standardisation to ensure robustness and reproducibility. This review presents an overview of the current state of automation of library preparation for next generation sequencing. Major challenges associated with library preparation are outlined and different automation strategies are classified according to their functional principle. Pipetting workstations allow high-throughput processing yet offer limited flexibility, whereas microfluidic solutions offer great potential due to miniaturisation and decreased investment costs. For the emerging field of single cell transcriptomics for example, microfluidics enable singularisation of tens of thousands of cells in nanolitre droplets and barcoding of the RNA to assign each nucleic acid sequence to its cell of origin. Finally, two applications, the characterisation of bacterial pathogens and the sequencing within human immunogenetics, are outlined and benefits of automation are discussed.

下一代测序正在从一种用于研究目的的技术发展为一种应用于临床诊断的技术。最近推出的高通量和台式仪器以较低的每碱基成本和更快的测定时间提供了全自动测序运行。反过来，复杂和繁琐的文库制备，从分离的核酸开始，并通过测序衔接子产生扩增和条形码化的DNA，已被确定为重大瓶颈。文库制备方案通常包括一个多步骤过程，需要昂贵的试剂和大量的动手时间。为了确保健壮性和可重复性，需要将重点放在标准化上。这篇综述概述了用于下一代测序的文库制备自动化的当前状态。概述了与库准备相关的主要挑战，并根据其功能原理对不同的自动化策略进行了分类。移液工作站允许高通量处理，但灵活性有限，而微流体解决方案由于小型化和降低的投资成本而具有巨大的潜力。例如，对于新兴的单细胞转录组学领域，微流控技术可以将纳升液滴中的数以万计的细胞单数化，并对RNA进行条形码编码，以将每个核酸序列分配给其起源细胞。最后，有两个应用，细菌病原体的表征和人类免疫遗传学中的测序，