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Navigating the Landscape of Different NGS Platforms: A Comprehensive Guide

Navigating the Landscape of Different NGS Platforms: A Comprehensive Guide

he development of next-generation sequencing (NGS) over the past 15 to 20 years has seen multiple technologies rapidly leapfrogging each other’s milestones to sequence more DNA faster, cheaper, and more accurately. While Illumina sequencers still predominate, other NGS providers are gaining ground, providing important alternative options for sequencing mechanisms, read lengths, run times, ease-of-use, and scalability. This article aims to guide researchers through the main differences among today’s common NGS platforms, with a special focus on the offerings from Capitalbio Technology.

The Evolution of NGS Sequencing Platforms

Next generation sequencing platforms have revolutionized genomics by enabling the sequencing of entire genomes quickly and cost-effectively. These platforms can be broadly categorized into short-read and long-read sequencing technologies, each with its own set of advantages and limitations.

Short-Read Sequencing Platforms

Short-read sequencing platforms typically sequence DNA fragments that are less than 300 bases long. These platforms have historically been higher in throughput and lower in cost compared to long-read sequencing. However, advancements in long-read technologies are closing this gap.


Illumina’s sequencing methods use a proprietary cluster generation process and sequencing-by-synthesis with fluorescently-tagged chain terminators. This has become the most widely adopted and published sequencing method, with more than 300,000 peer-reviewed publications. The longest read length of current Illumina platforms is 2x300, but the upcoming launch of Illumina® Complete Long-Read technology will enable researchers to generate contiguous long reads of 6–7 kb consistently, and up to 30 kb. Run times can vary from a few hours to 2 days, depending on the research project and the instrument used.

Thermo Fisher Scientific

Thermo Fisher Scientific’s Ion Torrent sequencing platforms perform NGS by measuring pH changes across millions of wells on a semiconductor chip during a sequencing run. Read lengths depend on the Ion Torrent system used: the Ion Torrent Genexus Integrated Sequencer is capable of up to 400 bp read lengths, and the Ion GeneStudio S5 System can produce up to 600 bp read lengths. Run times vary from 14–24 hours on the Ion Torrent Genexus Integrated Sequencer and from 3–24 hours on the Ion GeneStudio S5 Systems.

MGI/Complete Genomics

MGI, a global supplier of NGS and automation products, offers short-read sequencing products that have recently become more commercially available. They use DNA nanoball sequencing, in which fragments of gDNA or cDNA sample are amplified by rolling circle replication into DNA nanoballs, which are then arrayed at high density for sequencing. MGI platforms have maximum read lengths of SE400 for single reads and PE300 for paired reads. Typical run times can range from 12 hours to 3 days, depending on the sequencer model.

Long-Read Sequencing Platforms

Long-read sequencing, also known as single-molecule sequencing, sequences DNA fragments that are about 1 kb and above. These platforms offer several advantages, including the ability to distinguish large structural variations, regions of high homology or repetition, and splice variations.


PacBio’s Single-Molecule Real-Time (SMRT) technology sequences single DNA molecules immobilized at the bottom of tiny microwells using fluorescently tagged bases. PacBio’s HiFi sequencing, which uses circular consensus sequencing for 99.9% accuracy, offers long reads even in difficult-to-sequence regions of the genome. Read lengths typically range from 15 kb to approximately 40 kb, with run times of about 30 hours.

Oxford Nanopore Technologies

Oxford Nanopore Technologies’ sequencing technology centers around passing a single strand of DNA through a protein nanopore. The DNA sequence can be read by the ionic current moving through the pore. Oxford Nanopore’s platform can sequence DNA or RNA fragments of any length, from 30-base fragments to millions-of-bases fragments. The platform offers ultra-high throughput formats and portable, handheld instruments for sequencing in a wider range of applications.

Additional Considerations for NGS Platforms


Short-read sequencing is more prevalent and often less expensive, though single-molecule sequencing costs are becoming more competitive. The costs of NGS continue to decline, making it more accessible for various research applications.

Ease-of-Use and Scalability

Different NGS platforms vary in their ease-of-use and scalability. Illumina platforms are widely adopted, offering numerous published protocols and extensive support in research communities. Thermo Fisher Scientific and MGI also provide scalable solutions with varying run times and read outputs to meet different research needs. Oxford Nanopore’s portable devices offer unique advantages for sequencing outside traditional lab environments.

CapitalBio Technology: Pioneering Next-Generation Sequencing Services

At Capitalbio Technology, we are committed to advancing the field of genomics through innovative next-generation sequencing services. Our NGS platforms are designed to provide high-quality, reliable data for a wide range of applications, from clinical diagnostics to environmental research.

Next-Generation Sequencing Testing

Our next-generation sequencing testing services leverage the latest advancements in NGS technology to deliver accurate and comprehensive genomic data. Whether you need short-read or long-read sequencing, our platforms are equipped to handle diverse research requirements.

Next-Generation Sequencing Data Analysis

Data analysis is a critical component of NGS, and at Capitalbio Technology, we offer robust next-generation sequencing data analysis services. Our bioinformatics team utilizes advanced algorithms and software tools to ensure precise interpretation of sequencing data, enabling researchers to gain meaningful insights from their studies.

DNA Next-Generation Sequencing

Our DNA next-generation sequencing services cover a broad spectrum of applications, including whole-genome sequencing, targeted sequencing, and metagenomics. We provide end-to-end solutions, from sample preparation to data analysis, ensuring a seamless experience for our clients.

CapitalBio Technology Type Of Next Generation Sequencing Platforms(NGS Platforms)


Navigating the landscape of different NGS platforms can be challenging, but understanding the unique features and capabilities of each platform can help researchers make informed decisions. At Capitalbio Technology, we are dedicated to providing cutting-edge next-generation sequencing services and data analysis solutions to support your research endeavors. Whether you are exploring short-read or long-read sequencing, our comprehensive NGS platforms are designed to meet your specific needs and drive scientific discovery.

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