Next Generation Sequencing vs. Sanger Sequencing

What's the Difference?

Next Generation Sequencing (NGS) and Sanger Sequencing are two widely used methods for DNA sequencing. NGS is a high-throughput technique that allows for the simultaneous sequencing of millions of DNA fragments. It is faster, more cost-effective, and can generate a large amount of data in a single run. On the other hand, Sanger Sequencing is a traditional method that involves sequencing a single DNA fragment at a time. It is slower and more expensive compared to NGS but is still commonly used for sequencing shorter DNA fragments or for validating NGS results. While NGS is suitable for large-scale sequencing projects and identifying genetic variations, Sanger Sequencing is often preferred for smaller-scale projects or when high accuracy is required.


AttributeNext Generation SequencingSanger Sequencing
Sequencing MethodHigh-throughput parallel sequencingTraditional chain termination sequencing
Read LengthShort to long readsRelatively short reads
ThroughputHigh throughput, generates large amounts of dataLower throughput, generates less data
SpeedFast, can sequence millions of reads simultaneouslySlower, one read at a time
CostRelatively expensiveLess expensive
AccuracyLower accuracy due to shorter read lengthsHigher accuracy due to longer read lengths
ApplicationsWhole genome sequencing, transcriptome analysis, metagenomicsSequencing small genomes, targeted sequencing

Further Detail


Advancements in DNA sequencing technologies have revolutionized the field of genomics, enabling researchers to decipher the genetic code with unprecedented speed and accuracy. Two prominent methods used for DNA sequencing are Next Generation Sequencing (NGS) and Sanger Sequencing. While both techniques aim to determine the order of nucleotides in a DNA molecule, they differ significantly in terms of their approach, cost, throughput, and applications.

Principles of Next Generation Sequencing

Next Generation Sequencing, also known as high-throughput sequencing, encompasses a range of technologies that allow for the parallel sequencing of millions of DNA fragments. NGS platforms utilize various methods, such as Illumina sequencing, Ion Torrent sequencing, and Pacific Biosciences sequencing, to generate massive amounts of sequence data in a single run. These platforms rely on the amplification of DNA templates, followed by the incorporation of fluorescently labeled nucleotides and detection of emitted signals. The resulting data is then processed and analyzed to reconstruct the original DNA sequence.

Advantages of Next Generation Sequencing

One of the key advantages of NGS is its high throughput capability, enabling the simultaneous sequencing of multiple samples in a single run. This significantly reduces the time and cost required for sequencing large genomes or multiple samples. Additionally, NGS platforms offer greater sensitivity, allowing the detection of rare genetic variants and low-abundance sequences. The ability to generate vast amounts of sequence data also facilitates the analysis of complex genetic phenomena, such as gene expression profiling, epigenetic modifications, and metagenomics.

NGS also provides a more comprehensive view of the genome compared to Sanger sequencing. It allows for the identification of structural variations, such as insertions, deletions, and rearrangements, which are crucial in understanding the genetic basis of diseases. Moreover, NGS enables the sequencing of entire transcriptomes (RNA-Seq) and the exploration of non-coding regions, providing valuable insights into gene regulation and functional elements.

Limitations of Next Generation Sequencing

Despite its numerous advantages, NGS has some limitations that researchers must consider. The high error rate associated with certain NGS platforms can introduce inaccuracies in the generated sequences, particularly in regions with repetitive sequences or high GC content. Additionally, the short read lengths produced by some NGS technologies can pose challenges in assembling the complete genome sequence, especially for complex genomes or regions with repetitive elements.

Another limitation of NGS is the requirement for substantial computational resources and bioinformatics expertise to handle and interpret the massive amount of data generated. The analysis pipeline involves several steps, including quality control, alignment, variant calling, and annotation, which can be time-consuming and computationally intensive. Furthermore, the initial setup cost of NGS instruments and reagents can be relatively high, making it less accessible for smaller research laboratories or institutions with limited budgets.

Principles of Sanger Sequencing

Sanger sequencing, also known as chain termination sequencing, is a widely used method for DNA sequencing. It relies on the incorporation of chain-terminating dideoxynucleotides (ddNTPs) during DNA synthesis, resulting in the production of DNA fragments of varying lengths. These fragments are then separated by size using capillary electrophoresis, and the sequence is determined by detecting the emitted fluorescence from the labeled ddNTPs. Sanger sequencing is often employed for sequencing individual DNA fragments or verifying specific regions of interest.

Advantages of Sanger Sequencing

Sanger sequencing offers several advantages that make it a valuable tool in many research applications. It is known for its high accuracy, with error rates as low as one error per 1,000 bases. This makes it particularly useful for sequencing small regions or validating variants identified by NGS. Sanger sequencing also provides longer read lengths compared to most NGS platforms, allowing for the sequencing of larger DNA fragments or complete genes.

Another advantage of Sanger sequencing is its simplicity and ease of use. The workflow is straightforward, and the interpretation of results is relatively simple, making it accessible to researchers with limited bioinformatics expertise. Additionally, Sanger sequencing is often more cost-effective for small-scale projects or when sequencing a limited number of samples.

Limitations of Sanger Sequencing

While Sanger sequencing has its merits, it is not without limitations. The main drawback is its low throughput, as it can only sequence a single DNA fragment at a time. This significantly limits its utility for large-scale sequencing projects or when dealing with a high number of samples. The time and cost required for Sanger sequencing increase exponentially with the number of samples, making it impractical for many genomic studies.

Furthermore, Sanger sequencing is less sensitive compared to NGS, making it challenging to detect rare genetic variants or sequences present in low abundance. It is also less suitable for analyzing complex genetic phenomena, such as gene expression profiling or metagenomics, which require a higher depth of sequencing coverage.


In summary, Next Generation Sequencing and Sanger Sequencing are two distinct approaches to DNA sequencing, each with its own set of advantages and limitations. NGS offers high throughput, sensitivity, and comprehensive genomic coverage, making it ideal for large-scale projects and complex genetic analyses. On the other hand, Sanger sequencing provides high accuracy, longer read lengths, and simplicity, making it a valuable tool for targeted sequencing and validation of NGS results. The choice between these two methods ultimately depends on the specific research goals, budget, and available resources.

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