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DNA & NGS Library Quality Control and Quantification Tools


Sample Preparation |  Fragmentation  |  Fragment Size Selection  |  Quality Control  |  Library Preparation  |  Template Enrichtment/ Sequencing


High quality input DNA is important for optimal NGS library preparation and strong impacts sequencing results. Therefore, a number of different solutions for DNA quality control are available. Most instruments use fluorescence or UV/VIS based measurements in order to determine the purity and concentration of nucleic acids. Determination of DNA quality and purity is used in various steps before, during, and after DNA library preparation. Impure DNA can affect or inhibit downstream NGS library preparation steps.


A number of different DNA library quantification kits are available. Most solutions use PCR or qPCR amplification of the DNA library compared with an internal reference standard for quantification. Determination of exact DNA library concentration is very important for optimal template enrichment (e.g. template to bead ration during emulsions PCR), and for optimal cluster density and sequencing yield on the Illumina flow cell.


DNA Quality Control Instruments

Agilent 2200 TapeStation

The Agilent 2200 TapeStation system offers scalable throughput and rapid results, making it an ideal solution for quality control of biological samples in next-generation sequencing (NGS), microrarray, qPCR and aCGH workflows, as well as in protein purification and antibody production. The 2200 TapeStation system uses credit cardsized, disposable ScreenTape that is available for DNA, RNA and protein applications.

Source: Agilent

LabChip DS

The LabChip DS complements PerkinElmer's existing LabChip GX and LabChip GXII which provides fluorescent, electrophoretic analysis of fragments of nucleic acids and proteins. In addition, preparation of samples for the LabChip DS platform can be performed on PerkinElmer's liquid handling instruments, including the Sciclone® NGS Workstation, which is a robust, scalable platform that has been specifically customized for next generation sequencing methods, or PerkinElmer's Zephyr® Molecular Biology Workstation, which automates a broad range of standard molecular biology kits.
Source: PerkinElmer

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NanoDrop

Thermo Scientific NanoDrop instruments were the first microvolume UV-Vis spectrophotometers and fluorospectrometers designed specifically for the life science market and have fundamentally changed DNA, RNA and protein analysis. With more than 35,000 instruments in labs worldwide, NanoDrop instruments have become the recognized standard for microvolume instrumentation.
Source: Thermo Scientific

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QIAxpert System

QIAxpert is an innovative high-speed microfluidic UV/VIS spectrophotometer which profiles sample content to differentiate between DNA and RNA and sample impurities. QIAxpert is fast and easy to use, analyzing up to 16 samples within 2 minutes — just pipet samples onto the QIAxpert slide, place it into the reader, and select the pre-programmed method on the integrated touchscreen. QIAxpert is the right tool for any fast-paced lab performing nucleic acid quantification and quality control.
Source: Qiagen

QuantiFluor® dsDNA System

Whether you are quantitating your nucleic acids before or during library preparation, you need accurate, consistent and sensitive methods. Fluorescent quantitation is the method recommended by most NGS instrument and kit manufacturers.
Source: Promega

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Qubit™

Qubit™ fluorometric quantitation comprises the easy-to-use Qubit™ 3.0 Fluorometer and sensitive, specific Qubit™ quantitation assays. Based on the detection of target-specific fluorescence, this integrated system is more sensitive than UV absorbance–based quantification, making it ideal for precious samples and demanding applications.
Source: Thermo Fisher

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NGS Library Quality Control and Quantification Kits

ddPCR™ Library Quantification Kit

ddPCR™ Library Quantification Kit for Illumina/ Ion Torrent

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GeneRead DNA QuantiMIZE System

The GeneRead DNA QuantiMIZE System is a qPCR-based approach to determine quantity and quality of DNA that is amenable to amplification by targeted enrichment prior to NGS. The system has been developed for discovery, translational, and clinical researchers who need a cost-effective way to determine the optimum conditions for targeted enrichment of DNA isolated from biological samples, including FFPE.
Source: Qiagen

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GeneRead Library Quant System

The GeneRead Library Quant System provides a simple, out-of-the-box solution to quantify NGS libraries, enabling consistent results with every NGS run. The GeneRead Library Quant System uses real-time PCR to specifically quantify DNA molecules with sequencing adaptors at both ends, ensuring optimal cluster density or template-to-bead ratio.
Source: Qiagen

Ion Library Equalizer™

The Ion Library Equalizer™ Kit is a simple and seamless bead-based solution replacing the need for library quantification and library dilutions for library normalization as required for any next generation sequencing workflow. The Ion Library Equalizer™ Kit helps reduce labor, reagent costs, and further simplifies the Ion semiconductor sequencing workflow for high sample-throughput or barcoded projects, as well as single or low sample number projects.
Thermo Fisher

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Ion Library TaqMan™ Quantitation Kit

The Ion Library TaqMan™ Quantitation Kit is an easy-to-use, flexible solution for the accurate quantitation of library input for the Ion Torrent semiconductor sequencing workflow. This comprehensive kit provides a TaqMan® qPCR mix and library standard to detect and quantify femtomolar amounts of Ion Fragment Libraries. With universal cycling conditions that allow both fast and standard cycling, the Ion Library TaqMan Quantitation kit supports most real-time platforms. This universal kit provides greater accuracy and specificity compared to non-probe-based methods, delivering simplicity and speed to the PGM™ System sequencing workflow.
Source: Thermo Fisher

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Ion Sphere™ Quality Control Kit

The Ion Sphere™ Quality Control Kit furnishes a complete set of reagents for performing templated bead quality control using the Qubit® 2.0 Fluorometer. This comprehensive kit contains calibration controls, buffers, and a probe mix for quality assessment of pre-enriched and post-enriched template-positive Ion Spheres. The powerful combination of the Ion Sphere™ Quality Control Kit and the Qubit® 2.0 Fluorometer gives you greater experimental control and significant time and cost savings.
Source: Thermo Fisher

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Ion Universal Library Quantitation Kit

The Ion Universal Library Quantitation Kit is an easy-to-use, flexible solution for the accurate quantitation of library input generated by the Ion 16STM Metagenomics Kit for Ion Torrent™ semiconductor sequencing. This kit provides the TaqMan® assay, TaqMan® Universal Master Mix, and library standard needed to quantify femtomolar amounts of Ion fragment libraries. With cycling conditions that allow both fast and standard cycling, the Ion Universal Library Quantitation Kit supports most real-time platforms. This real-time PCR kit enables greater accuracy and specificity compared to non-PCR or non-probe-based methods, delivering simplicity and speed to the Ion PGM™ System sequencing workflow.
Source: Thermo Fisher

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KAPA Library Quantification Kits

KAPA Library Quantification Kits contain all the reagents needed for the accurate, reliable and reproducible qPCR-based quantification of NGS libraries prior to pooling for capture or flow cell amplification. Kits contain KAPA SYBR® FAST qPCR Master Mix, optimized for high-performance SYBR Green I-based qPCR. The engineered KAPA SYBR FAST DNA Polymerase contained in the Master Mix amplifies GC- and AT-rich DNA fragments of different lengths with similar efficiency, making it the only qPCR Master Mix capable of accurate qPCR-based quantification of NGS libraries. The pre-diluted set of DNA Standards contained in each kit is carefully quality-controlled to ensure lot-to-lot consistency and avoid data drift over time. Optimized Primer Premixes ensure optimal PCR efficiency.
KAPA Biosystems

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NEBNext Library Quant Kit

The NEBNext Library Quant Kit delivers significant improvements to qPCR-based library quantitation for next gen sequencing. The NEBNext Library Quant Kit for Illumina contains components that are optimized for qPCR-based quantitation of libraries prepared for Illumina next-generation sequencing platforms. The NEBNext Library Quant Kit contains primers which target the P5 and P7 Illumina adaptor sequences and a set of high-quality, pre-diluted DNA standards to enable reliable quantitation of diluted DNA libraries between 150–1000 bp.
Source: NEB

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NGS FFPE QC Kit

The Agilent NGS FFPE QC kit is a qPCR-based assay that enables functional DNA quality assessment of input DNA prior to preparation of next generation sequencing libraries. This kit enables assessment of the integrity of DNA as well as accurate quantitation of amplifiable template going into library preparation. Furthermore, optimizations to the SureSelectxt workflows based on the sample quality score are enabled.
Source: Agilent

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NGS Library Quantification Kit

NGS Library Quantification Kit To obtain high-quality Illumina® next-generation sequencing (NGS) data, loading the flow cell with an appropriate amount of library DNA is essential. Loading an insufficient amount of library DNA will result in low cluster density and reduced sequencing yield; an overabundance of library DNA may increase cluster density and result in poor quality data. Standard methods of NGS library quantification, such as those based on electrophoresis or spectrophotometry, have low sensitivity, are non-specific for adapter-bound DNA, and typically require a large amount of library sample for analysis. The Library Quantification Kit provides a highly-sensitive, qPCR-based quantification method that specifically targets adapter sequences used for Illumina’s NGS reactions. This kit allows specific measurement of the sequencing library concentration even in samples that contain DNA molecules not bound to adapters. This kit can also be used to confirm adapter ligation during library preparation.
Source: Clontech

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Ovation 3'-DGE System

The Ovation 3'-DGE System provides accurate expression analysis (tag profiling) suitable for quantification of any poly(A)+ transcripts, without the need for prior sequence knowledge. It employs a simple, fast and automatable workflow, powered by the Ribo-SPIA® Single Primer Isothermal Amplification technology and is compatible with all leading NGS platforms.
Source: Nugen

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Quant-iT™ High-Sensitivity DNA Assay Kit

The Quant-iT™ High-Sensitivity DNA Assay Kit makes DNA quantitation easy and accurate. The kit provides concentrated assay reagent, dilution buffer, and pre-diluted DNA standards. The assay is highly selective for double-stranded DNA over RNA, and in the range of 0.2-100 ng of DNA, the fluorescence signal is linear.
Source: ThermoFisher

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