AAT Bioquest

When do I use Sanger sequencing vs NGS?

Posted February 9, 2022


The concepts behind Sanger sequencing vs. NGS (Next-Generation Sequencing) technologies are similar in principle. In both processes, fluorescent nucleotides are added one at a time onto a growing DNA template strand by DNA polymerase. The major difference between the two is the sequencing volume.

Sanger sequencing only sequences one DNA fragment at a time. On the other hand, NGS is massively parallel, sequencing millions of fragments simultaneously. NGS also offers greater discovery power for the detection of novel or rare variants.

Sanger sequencing is the preferred technique for:

  • Sequencing up to 96 samples at a time without barcoding
  • Microbial identification
  • Sequencing 1-100 amplicon targets at the lowest cost
  • Microsatellite or STR analysis
  • Fragment analysis
  • NGS confirmation

NGS is the preferred technique for:

  • Cost-effective sequencing of hundreds to thousands of gene or gene regions simultaneously
  • Faster turnaround times for high sample volumes
  • Sequencing samples with low input amounts of starting material
  • Comprehensive genome coverage
  • Identifying novel, low-frequency variants by expanding the number of targets sequenced in a single run


Additional resources

Standardized next-generation sequencing of immunoglobulin and T-cell receptor gene recombinations for MRD marker identification in acute lymphoblastic leukaemia; a EuroClonality-NGS validation study

MagaDye™ 535-ddGTP

Coronavirus (SARS-CoV-2)