QIAxcel Advanced System as an instrument for NGS library quality control analysis

QIAxcel Advanced

The quality of the NGS library is a critical factor for the success of the sequencing run, affecting both the sequence validity and the number of reads. Quality control procedures of library preparation ensure that only samples of good quality are processed and sequenced to generate reads of the highest quality that can be confidently turned into valuable insights.

In addition to the traditional agarose gel electrophoresis method, capillary electrophoresis systems, such as the QIAxcel Advanced System, are available. This automation method eliminates the need for tedious gel preparation and reduces manual handling errors, ensuring reproducibility of the analysis.

Recently QIAGEN scientists compiled a new study in collaboration with the Agency for Science, Technology and Research at the Genome Institute of Singapore, to evaluate the performance of the QIAxcel Advanced System and another well-established capillary electrophoresis system  – the Agilent 2100 Bioanalyzer System – to explore whether the QIAxcel Advanced System produces comparable NGS library size calling to the Bioanalyzer. For this study, a total of 90 NGS libraries of different library types were analyzed on both systems.

QIAxcel figure 1



The diversity and ratios of the different library types and library prep kits used in this study are shown as an illustration (Figure 1).

The linear regression analysis shows a strong correlation of the library sizes determined by the QIAxcel and the Bioanalyzer with a coefficient of correlation R2 = 0.954 (Figure 2a).

The Bland-Altman analysis of the size determination of the QIAxcel and the Bioanalyzer also shows a strong agreement between the two systems with a mean difference of only 7 bp ± 19 bp with determined library sizes between 205 bp and 562 bp (Figure 2b). The average percentage difference for the complete data set falls below 2%.


QIAxcel figure 2

The study demonstrates that the QIAxcel Advanced System can be used for NGS library quality control analysis for various library types, such as libraries for Whole Genome Sequencing, Whole Exome Sequencing, ChIP seq, RNA seq and metagenomic seq.

QIAxcel Advanced System produces a comparable NGS library size calling to the Agilent 2100 Bioanalyzer System. Furthermore, the study results demonstrate consistency in NGS library size determination regardless of the library type and library preparation kit used.

With its fast processing time, ready-to-run cartridges and the ability to analyze up to 96 samples automatically, the QIAxcel Advanced System is a superior system in respect of efficiency, reproducibility and cost per sample for NGS library QC analysis (see also comparison table below).

QIAxcel table


Download the full application note to get all the details here and/ or watch our how-to videos to get answers to FAQ’s about the QIAxcel Advanced System.

Disclaimer: The products mentioned are for Molecular Biology Applications Only. Not for the diagnosis, prevention or treatment of a disease.

Kjell Kirschbaum

Kjell Kirschbaum, M.Sc., is a Global Market Manager based in QIAGEN’s Venlo office, the Netherlands. He trained as a bioveterinary scientist at the University of Utrecht and has hands-on experience in nucleic acid and protein purification, cell culture, PCR and qPCR technology. Kjell joined QIAGEN in 2011 as a CRM specialist, regularly interacting with customers about their day-to-day experimental needs and offering relevant solutions. Currently, he is involved in managing global projects for sample preparation and automation technologies.

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