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Detection of adapter dimers in NGS libraries with the Agilent Fragment Analyzer and TapeStation Systems

Agilent Technologies
5 Jun 2023

In this application note, Agilent Technologies explains the significance of minimizing adapter dimers in NGS libraries before sequencing. Adapter dimers are formed when two adapters ligate to each other without any insert, leading to erroneous sequencing data. Even small amounts of adapter dimers can cause detrimental sequencing results by affecting library quantification, flow cell loading, clustering efficiency, diversity, and genome coverage. In this note, Agilent's Fragment Analyzer and TapeStation Systems is introduced as a way to accurately and reliably detect adapter dimers below the recommended threshold of 0.5%, providing valuable data to evaluate library quality and make important decisions regarding subsequent analysis.

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Fragment Analyzer Systems

Agilent Technologies

The Agilent Fragment Analyzer systems are fluorescence-based capillary electrophoresis instruments for the accurate sizing, quantification, and qualification of nucleic acids (DNA and RNA).

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DNA / RNA Extraction and PurificationPurified DNA and RNA are required for numerous downstream molecular biology applications. Consequently, the importance of high-quality DNA/RNA extraction and purification equipment cannot be underestimated. Many purification kits are available and are typically optimized for nucleic acid type and source, including plasmid DNA, genomic DNA, mRNA, RNA and viral nucleic acid purification kits. Automated extraction and purification of nucleic acids can be implemented with magnetic bead separator instruments or high-throughput purification workstations. Find the best DNA/RNA extraction and purification 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.DNA ExtractionDNA extraction is a critical step in many biological studies, including genomics, diagnostics, and forensic analysis. The process involves isolating DNA from cells or tissues, and the quality and purity of the extracted DNA can impact downstream applications. Explore DNA extraction products in our peer-reviewed product directory; compare products, check reviews, and get pricing directly from manufacturers.DNADeoxyribonucleic Acid (DNA) is the main component of chromosomes and the carrier of genetic information of living organisms. Find out here about PCR, NGS, ChIP-Seq, gel imaging, and many other techniques which can be used for the analysis of DNA.Clinical NGSNext Generation Sequencing (NGS) refers to the use of massive parallel sequencing of multiple small fragments of DNA. This high-throughput genomic analysis yields enormous amounts of sequence data, which if appropriately analyzed could have huge potential for clinical laboratories. For this to happen there are technique and bioinformatic hurdles to be overcome.

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Detection of adapter dimers in NGS libraries with the Agilent Fragment Analyzer and TapeStation Systems