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Quality control of NGS libraries with daisy chains

Agilent Technologies
17 Jun 2025

The Agilent automated electrophoresis solutions offer fast and reliable quality control of next-generation sequencing (NGS) libraries. The Bioanalyzer, TapeStation, and Fragment Analyzer systems with dedicated high sensitivity assays allow unambiguous detection of daisy chains and accurate sizing of the target library. In this application note, Agilent Technologies provides a recommendation for which assay to employ to reliably visualize daisy chain products in NGS libraries. Furthermore, it emphasizes the consistency between the instruments and reproducibility of analysis confirmed by results on a set of two-fold serial dilutions.

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4200 TapeStation Instrument

Agilent Technologies

The Agilent 4200 TapeStation system is an established automated electrophoresis tool for DNA and RNA sample quality control. Fully automated sample processing enables the unattended analysis of size, concentration and integrity. Choose any sample number between 1 and 96 and analyze at constant cost per sample.

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ElectrophoresisElectrophoresis equipment is used to separate mixtures of protein, DNA or RNA, based on their electric charge, size and other physical characteristics, by passing them through a medium such as a polyacrylamide gel, an agarose gel or a capillary tube. Electrophoresis equipment includes horizontal and vertical gel electrophoresis chambers, isoelectric focusing systems, 2D electrophoresis and capillary electrophoresis instruments. Precast gels with a gradient can be used or gels can be hand cast. Samples are run alongside ladders or markers to identify the approximate size of a molecule. Separated proteins and nucleic acids in the gel can be stained or probed with fluorescent markers and then imaged and detected using gel documentation instruments, transilluminators, densitometers and scanners. Find the best electrophoresis equipment in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Next Generation SequencingNext-generation sequencing (NGS), also known as whole-genome sequencing, high-throughput sequencing and massive parallel sequencing, produces and analyses thousands to millions of nucleotide sequences at once. Sequencing systems operate via varying technologies depending on the manufacturer, including sequencing by synthesis, ligation, pyrosequencing, ion semiconductor and single-molecule real-time sequencing. For NGS, library preparation is paramount to successful sequencing. In this section, explore a range of library preparation kits, from targeted, amplicon-based or hybridization-based kits including epigenomic, transcriptomic and genomic workflows to fragmentation kits. Find the best next-generation sequencing products in our peer-reviewed product directory: compare products, check customer reviews and receive pricing direct from manufacturers.Quality ControlQuality control is needed in all production processes. Quality control is a monitoring procedure or set of procedures that are put in place to ensure that a manufactured product adheres to a defined set of quality criteria. AutomationAutomation in laboratories and manufacturing processes enhances efficiency, precision, and scalability by reducing the need for manual intervention. It plays a critical role in improving productivity, minimizing human error, and accelerating workflows in fields like diagnostics, drug development, and industrial testing. Automation technologies include robotic systems, automated liquid handlers, and process control systems that streamline complex tasks and ensure consistent, reproducible results. Explore our peer-reviewed product directory to discover the best automation solutions, compare options, read user reviews, and get prices directly from manufacturers.Electrophoresis

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