AAT Bioquest

What are the differences between next-generation sequencing (NGS) and qPCR?

Posted February 18, 2022

Basis of DifferencesNext-Generation Sequencing (NGS)qPCR
Discovery power or ability to identify novel variantsOffers considerably higher discovery power enabling detection of novel variations. Also offers higher sensitivity enabling quantification of rare variants and transcriptsVery poor discovery power. Is capable of detecting only known sequences.
Scalability and throughputOffers higher sample throughput – a single NGS experiment is capable of identifying variants across numerous target regions with single base resolutionOffers lower scalability - is more effective for lower target numbers. Even then, the workflow can be unwieldy for multiple targets. Enables interrogation of a limited set of variants.
Cost effectivenessLess cost-effective for sequencing lower numbers of targets (1–20 targets).More cost effective when the number of target regions is less than 20 targets and when the study aims to screen or identify known variants.

Whether NGS or qPCR is better for you will depend on a variety of factors including the number of samples, study goals, total amount of sequence in the target regions, and budgetary considerations.

Additional resources

High Throughput Sequencing: An Overview of Sequencing Chemistry

TAQuest™ qPCR Master Mix with Helixyte™ Green *No ROX*