When to Choose Capillary Electrophoresis for Genomic Analysis

Sanger sequencing, next generation sequencing (NGS), long read sequencing, and fragment analysis each enable a variety of applications across a broad range of research areas. Both Sanger sequencing and fragment analysis use capillary electrophoresis (CE) for separation and detection. The method of choice depends on your application and throughput.

CE, long read, or NGS? How to choose the right sequencing method

Sanger sequencing is ideal for small-scale projects focusing on one or two genes, while NGS is ideal for higher-throughput sequencing needs. Long read sequencing is useful for the discovery of large unknown variants. Although fragment analysis does not provide sequence information, it is a simple and accurate method used to generate relative quantitation information in a cost-effective manner due to its high resolution and multiplexing capability.

Here are some things to consider when deciding the right sequencing method for your needs:


Sanger sequencing


Long read sequencing

 Requires a known priming site

Yes, needs known DNA sequence.

No, unknown DNA sequence for de novo sequencing

No, unknown DNA sequence for de novo sequencing

Error rate


Considered gold-standard for accuracy



Read length

20-1400 bp

50-500 bp

20-100,000 bp

Number of targets recommended




Full run time


hours - days






Recommended Applications

  • Known plasmid sequencing 
  • Organism genotyping 
  • Single gene errors 
  • Small Indels 
  • Challenging templates (like high GC) 
  • Confirmation
  • Discover novel variants
  • Organism genotyping 
  • Oncology screening panels 
  • Liquid biopsy 
  • Epigenetics 
  • RNA sequencing
  • HLA 
  • Complex re-arrangements 
  • Haplotype phasing 
  • Large structural variants 
  • Epigenetics

 *based on recent publications

Fragment analysis


Fragment analysis leverages the single base resolution of CE to detect hundreds of targets per reaction. It is useful for many applications, including:

  • SNP detection
  • STR analysis
  • Tandem repeat analysis
  • Methylated DNA analysis


Frequently asked questions

Both Sanger sequencing and fragment analysis utilize capillary electrophoresis to provide simple, sample-to-answer workflows for highly accurate sequence interrogation and fast turnaround time.

Sanger sequencing

  • Study a small subset of genes linked to a defined phenotype
  • Confirm NGS variants
  • Detect minor allele fractions down to 5%
  • Read contiguous sequences up to 1000 bases

Learn the basics of Sanger sequencing:

Fragment analysis

  • Provides sizing, relative quantitation, and genotyping information; does not require sequence knowledge of fragment
  • Multiplexing capability
  • MSI marker analysis
  • Gene editing efficiency
  • SNP genotyping

Learn the basics of fragment analysis:

From genetic disease and cancer research to cell line authentication and forensic science, capillary electrophoresis continues to advance scientific research across various fields.

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