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	NGS	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	0.001% Considered gold-standard for accuracy	0.1–0.6%	0.1–7%*
Read length	20-1400 bp	50-500 bp	20-100,000 bp
Number of targets recommended	<20	>20	>20
Full run time	hours	hours - days	days
Cost/sample	$	$$-$$$	$$-$$$
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:

Download the Sanger Sequencing Guide

See more Sanger Sequencing applications

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:

Download the Fragment Analysis Application Guide

See more fragment analysis applications

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

Explore highlights of several powerful Sanger sequencing and fragment analysis applications

Explore more fragment analysis applications

Explore more Sanger sequencing applications