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NGS or Sanger sequencing: an easy guide for choosing the right technology

Find out which DNA sequencing technology is right for finding answers to your questions.

Posted 4 March 2022

In short: Sanger sequencing is a fast, reliable and cost-effective method when looking at a low numbers of short genomic regions. Next generation sequencing (NGS) can examine large genomic regions very efficiently – for example whole genomes or exomes.


What are the differences between Sanger and NGS?

Although both techniques analyze DNA at the single-base level the approach is different in many ways.

Sanger sequencing relies on the dye termination method, first described by Frederic Sanger. It creates fragments of the sequence of interest, all starting from a primer but terminated at different lengths. The end of each fragment has a fluorescent label, with different colors for the A, C, G and T nucleotides. These fragments are detected after separating the different sizes by capillary electrophoresis – which is why it’s also known as capillary electrophoresis sequencing (CES).

The term NGS usually refers to a wide range of different techniques that sequence DNA libraries. These large collections of short DNA fragments (most often 100s of bases long, but up to 10.000s is possible) can come from fragmented genomic DNA or RNA, amplicons, or even mixed genome fragments from multiple species (metagenomes). In this high-throughput method all sequences in a library are sequenced together – and bioinformatics analysis is used to reconstruct the full original sequence(s).


When to use Sanger sequencing?

The strength of Sanger sequencing lies in the analysis of sequences of 100s to 1000s of bases. Here, Sanger’s unrivaled accuracy is a key benefit over other molecular techniques. Key applications for Sanger sequencing include finding single nucleotide polymorphisms (SNPs) in known locations, species identification by studying for example 16S rRNA and many others.

Sanger sequencing also comes with a shorter workflow, making it suitable for applications where a speedy result is essential. At Macrogen Europe for example, we offer Sanger sequencing turnaround times as low as 24 hours.


When to use NGS?

Next generation sequencing is the technology of choice when looking at large regions of the genome, the transcriptome or the epigenome. Its ability for ‘massively parallel’ sequencing makes it possible study everything from targeted gene panels to whole genomes and whole exomes with stunning efficiency.

NGS also excels in metagenomics, which studies all the species present in a mixed sample. This approach is useful for example in microbiome samples where NGS can identify species with 16S amplicon sequencing – or even study whole genomes with meta-shotgun sequencing.


At Macrogen Europe, we provide a wide range of Sanger sequencing and NGS services. So if you’re unsure about which technique is the best for your situation, get in touch now for a free consultation to find out the optimal solution for you.