Third Generation Sequencing Market By Technology (Single Molecule Real-Time Sequencing, Nanopore Sequencing); By Application (Genomics & Epigenomics, Transcriptomics, Oncology, Infectious Disease Diagnostics, Rare Disease Detection, Agrigenomics, Neurodegenerative Research); By End User (Academic & Research Institutions, Pharmaceutical & Biotech Companies, Clinical Diagnostics Laboratories, Agricultural Genomics Facilities); By Geography, Segment Revenue Estimation, Forecast, 2024–2030

Introduction And Strategic Context

The Global Third Generation Sequencing Market is projected to grow at a compelling CAGR of 18.5% , with an estimated market value of USD 2.1 billion in 2024 , expected to reach USD 5.8 billion by 2030 , according to Strategic Market Research.

 

Third generation sequencing (TGS) — also known as long-read sequencing — represents a significant leap beyond the short-read technologies that defined the last decade of genomics. It enables real-time, high-throughput sequencing of single DNA molecules without the need for amplification. That single capability is changing how scientists approach everything from rare disease diagnosis to plant genome research.

 

Strategically, the appeal of TGS isn’t just accuracy. It’s the depth of insight. Whether it’s capturing complex structural variants, phasing haplotypes, or decoding epigenetic modifications, third generation sequencing opens up research that was once impractical or impossible using earlier methods. And now that pricing is starting to decline and sample prep workflows are being streamlined, adoption is spilling beyond elite genomics labs into core clinical, agricultural, and pharmaceutical applications.

 

Governments are also leaning in. The U.S. National Institutes of Health (NIH) and China’s National Genomics Data Center are both expanding long-read-based reference genome programs. Meanwhile, regulatory bodies are beginning to outline frameworks for clinical use — especially in oncology and rare disease detection. That institutional shift is likely to accelerate market validation and broader reimbursement traction.

 

The ecosystem around TGS is also maturing. Hardware providers are refining accuracy and run-time efficiency. Reagent suppliers are focusing on multiomic compatibility. Bioinformatics players are tailoring pipelines for long-read datasets. And pharma companies are piloting TGS in companion diagnostics and biomarker discovery.

 

In short, third generation sequencing is no longer just a research tool. It’s becoming a translational engine — one that could redefine personalized medicine, environmental metagenomics, and next-gen synthetic biology pipelines.

 

Unlike earlier sequencing waves that democratized access to genetic data, this one is all about completeness. And for many stakeholders, that makes it the most strategic leap yet.

 

Market Segmentation And Forecast Scope

The third generation sequencing market cuts across multiple layers of application, end user, and technology — each reflecting how stakeholders harness long-read sequencing to push scientific and clinical boundaries. Here’s how the segmentation typically unfolds:

By Technology

• Single-Molecule Real-Time (SMRT) Sequencing

• Nanopore Sequencing

SMRT sequencing — pioneered by Pacific Biosciences — remains dominant in terms of accuracy and has gained traction in complex genome assembly, epigenetics, and full-length RNA sequencing. As of 2024, SMRT accounts for approximately 61% of the market revenue.

Nanopore sequencing , developed by Oxford Nanopore Technologies, is growing faster — especially in field-based and portable applications. Real-time data output and scalability make it appealing for both research labs and point-of-care genomics. Expect nanopore’s share to rise rapidly, particularly in infectious disease surveillance and real-time transcriptomics.

 

By Application

• Genomics & Epigenomics

• Transcriptomics

• Oncology

• Infectious Disease Diagnostics

• Agrigenomics

• Rare Disease Detection

• Neurodegenerative Research

Rare disease diagnostics and oncology are the twin engines of growth. These applications demand deeper structural insight and phasing capabilities — areas where long-read platforms outperform. Meanwhile, plant and microbial genomics continue to be major use cases in academic research and ag-biotech.

 

By End User

• Academic & Research Institutions

• Pharmaceutical & Biotech Companies

• Clinical Diagnostics Laboratories

• Government & Regulatory Bodies

• Agricultural Genomics Facilities

Academic labs were the early adopters. But the real momentum now lies with pharma and clinical diagnostics labs , which are expanding their use of TGS in companion diagnostics, biomarker discovery, and population-scale genomics programs.

For example, a leading oncology diagnostics lab in Germany adopted long-read sequencing to identify fusion genes in complex sarcoma cases — improving both turnaround time and treatment precision.

 

By Region

• North America

• Europe

• Asia Pacific

• Latin America

• Middle East & Africa

North America leads the market, thanks to high R&D budgets, a strong base of genomics companies, and growing integration into clinical workflows. Asia Pacific , however, is the fastest-growing region — driven by government genome initiatives, rising biotech funding, and aggressive expansion by Chinese sequencing companies.

 

Forecast Scope

This report covers market estimates and projections from 2024 to 2030 , analyzing growth trends across all major technologies, end users, and geographies. While SMRT holds majority share today, nanopore sequencing is expected to outpace it in CAGR terms , particularly in resource-constrained and mobile settings.

What makes this market commercially interesting is its dual-curve: a research base that’s steady and diversified , paired with an emerging clinical curve that’s poised for exponential scaling.

 

Market Trends And Innovation Landscape

The third generation sequencing (TGS) market is evolving quickly — not just in terms of throughput or read lengths, but in how the entire ecosystem is being re-engineered to fit into real-world research, clinical, and industrial workflows. What began as an ultra-niche innovation is now unlocking broader use cases through smarter chemistry, faster informatics, and plug-and-play platforms.

1. Precision is No Longer Optional — It's Table Stakes

One of the most important shifts in TGS is the push to improve accuracy without compromising on read length or speed. Earlier criticism around error rates — particularly in nanopore sequencing — is being addressed by algorithmic corrections, adaptive sampling, and real-time basecalling enhancements.

PacBio’s HiFi reads and Oxford Nanopore’s duplex sequencing are narrowing the accuracy gap with short-read platforms. Now, labs can get Q20+ reads (99%+ accuracy) without fragmenting DNA, making long-read sequencing not just viable, but competitive in regulated environments.

“We used to run Illumina for reliability and long-read tech for discovery. Now we’re seeing both in one workflow,” said a genomics director at a cancer institute in California.

 

2. Real-Time Sequencing is Shaping New Use Cases

One of TGS’s standout features is real-time sequencing and analysis . That’s changing how clinicians and field researchers think about diagnostics and surveillance.

• In infectious disease outbreaks, nanopore sequencers are already being deployed to remote locations to sequence and analyze viral genomes within hours.

• Clinical labs are beginning to adopt TGS in same-day hematological malignancy profiling — bypassing multi-step PCR and FISH workflows.

As turnaround time shrinks, TGS is gaining interest in ER-based genomic triage, neonatal screening, and even forensic biology.

 

3. Multiomic Integration is Moving from Buzzword to Blueprint

The genomics world is quickly shifting toward multiomic profiling — combining DNA, RNA, methylation, and protein-level data. Long-read platforms are uniquely positioned here:

• SMRT and nanopore technologies can detect base modifications like 5-methylcytosine directly — no bisulfite conversion needed.

• Full-length transcript sequencing (Iso-Seq, direct RNA-seq) enables more accurate gene expression and isoform analysis.

That’s opening doors in neuroscience, autoimmune disease profiling, and early-stage cancer detection — where complex regulatory signatures matter more than just mutations.

 

4. Cloud-Based Bioinformatics is Removing the Bottleneck

The raw power of TGS is only as good as the downstream analysis. That’s why cloud-native bioinformatics is gaining traction. Platforms like DNAnexus and Terra are being integrated directly with sequencers, enabling:

• Real-time basecalling and quality control

• Structural variant detection at population scale

• AI-assisted annotation and visualization

These tools are increasingly tuned to handle large, noisy, or methylation-rich datasets — a key value driver in epigenetics and oncology.

 

5. Innovation is No Longer Vendor-Led — It’s Ecosystem-Driven

The TGS innovation wave is now being co-developed across multiple fronts:

• Academic Labs are publishing new epigenetic workflows and open-source alignment tools.

• Startups are building plug-in informatics pipelines, variant annotation engines, and methylation-specific callsets.

• Pharma is co-funding TGS-based companion diagnostics in oncology and immunology.

• Ag-biotech players are creating population-scale genotyping-by-sequencing models for plants and livestock.

To be honest, third generation sequencing is no longer just about hardware specs. It's about who can build an ecosystem that delivers insights at clinical-grade quality — fast.

Bottom line: We’re now in a phase where the tech itself is stable — and the race is about speed to application. The real innovation isn’t just in better chemistry or longer reads. It’s in seamlessly integrating those capabilities into the way clinicians, researchers, and public health agencies work every day.

 

Competitive Intelligence And Benchmarking

The third generation sequencing (TGS) market is dominated by a handful of high-profile players — but the real story is how differently each is approaching scale, accuracy, and end-user alignment. Unlike the short-read era, where platforms were fairly interchangeable, TGS is seeing sharp strategic divergence: one side focused on precision and depth, the other on flexibility and portability.

Pacific Biosciences (PacBio)

PacBio remains the category-defining company in high-fidelity long-read sequencing. Its SMRT (Single Molecule Real-Time) technology, especially the HiFi sequencing platform , is considered the gold standard for read accuracy and uniformity across genome types. In 2024, PacBio has focused on expanding applications in rare disease diagnosis , plant genomics , and whole-transcriptome sequencing .

• Stronghold in clinical-grade applications , with growing traction in Europe and Japan.

• Strategic partnerships with hospitals and academic centers for long-read cancer screening pipelines.

• Recently launched cloud informatics suites tailored for HiFi datasets.

Their strategy is clear: dominate in any setting where accuracy is non-negotiable.

 

Oxford Nanopore Technologies

On the other end of the spectrum is Oxford Nanopore , which offers the most flexible and portable sequencing systems on the market. Their nanopore-based tech is the only one that delivers real-time, plug-and-play sequencing on desktop or handheld devices — including the MinION and PromethION series.

• Gaining rapid adoption in infectious disease surveillance, microbial genomics, and agricultural labs.

• Major presence in low-resource settings due to affordable setup and low maintenance.

• Partnered with multiple global health agencies for field-based epidemic monitoring.

They've also doubled down on epigenetics and direct RNA sequencing , positioning themselves as a full-spectrum multiomic provider.

Their edge? Accessibility and scale — from labs to field stations.

 

QIAGEN

QIAGEN is carving a niche through workflow integration . Rather than building sequencers from the ground up, the company offers sample prep, library construction kits, and bioinformatics platforms optimized for long-read sequencing .

• Collaborated with PacBio and Oxford Nanopore to create plug-and-play sample prep systems.

• Offers QIAseq kits for full-length transcriptome analysis and methylation profiling.

• Recently expanded their digital bioinformatics platform to include AI-guided annotation for structural variants.

They’re not competing on sequencing hardware — they’re becoming the connective tissue of the ecosystem.

 

Illumina (Indirect Competitive Force)

While Illumina doesn’t offer third generation systems, it remains the incumbent benchmark in short-read sequencing. However, its indirect presence still matters:

• Some labs run TGS alongside Illumina for validation or hybrid assembly.

• Illumina’s push into pan-genomics and oncology diagnostics may pressure TGS vendors to accelerate clinical readiness.

• Regulatory delays and market saturation in short-read workflows have led some customers to explore TGS as a complementary or alternative path.

In many ways, Illumina sets the standard TGS players are trying to redefine — and then exceed.

 

Other Players & Startups

Several early-stage companies and academic spinoffs are making quiet but meaningful inroads:

• Stratos Genomics (acquired by Roche) had been working on sequencing-by-expansion chemistry that blends nanopore ideas with polymer physics.

• GenapSys has dabbled in compact sequencing platforms, aiming for hospital-grade simplicity, though commercial traction remains limited.

• Multiple AI-bioinformatics startups now offer TGS-optimized variant detection and epigenomic interpretation tools .

While these smaller players don’t yet pose a direct threat, their innovations often shape how the big two — PacBio and Oxford Nanopore — prioritize roadmap features and user workflows.

 

Regional Landscape And Adoption Outlook

Adoption of third generation sequencing (TGS) is playing out very differently across regions — shaped not just by funding levels, but also by national genomics strategies, healthcare infrastructure, and local biotech ecosystems. In some countries, TGS is already part of precision medicine pipelines. In others, it's still largely research-focused. Let’s unpack the current landscape.

North America

The U.S. is, by far, the most mature and well-funded market for TGS. Key drivers include:

• Large-scale genomics programs , such as the NIH’s All of Us initiative and NCI’s Cancer Moonshot, which increasingly include long-read sequencing components.

• A deep biotech and diagnostics ecosystem across hubs like Boston, San Diego, and San Francisco — many of which now require TGS for structural variant profiling and transcriptomics.

• Strong clinical adoption signals , especially in rare disease diagnostics and oncology.

Canada is catching up, with public health labs starting to integrate long-read tech into pathogen surveillance and population genomics programs.

To be honest, North America’s lead isn’t just tech access. It’s the regulatory and reimbursement shift now starting to favor long-read tools in clinical genomics.

 

Europe

Europe is diverse in terms of adoption, but several key countries are showing leadership:

• Germany and the UK are investing heavily in national rare disease programs and cancer screening initiatives that use long-read sequencing for its structural resolution.

• The EU Horizon Europe program is funding cross-border genomic research that includes TGS platforms.

• France and the Nordics are using long-read systems for pharmacogenomics , neurodegenerative disease profiling , and longitudinal cohort studies .

That said, regulatory conservatism and public health bureaucracy can slow down clinical adoption — especially compared to the U.S.

Still, Europe remains a critical innovation hub, especially for bioinformatics startups and integrated diagnostic platforms that complement long-read workflows.

 

Asia Pacific

This is the fastest-growing region — not just in sequencing output, but in policy-driven genomics acceleration.

• China is scaling rapidly. Long-read sequencing is being integrated into:

• National rare disease diagnostics programs

• Agricultural genomics (rice, maize, pigs)

• Infectious disease monitoring at regional centers

• Japan is investing in epigenomic medicine and direct RNA sequencing as part of its precision medicine roadmap.

• India is still early-stage but ramping up, especially in research centers and large hospital networks. Interest is growing in using TGS for:

• Tuberculosis strain tracking

• Pharmacogenomic screening

• Rare genetic disorder research in consanguineous populations

The presence of local manufacturing and reagent sourcing in China and South Korea is also helping reduce cost barriers for adoption.

Asia Pacific’s trajectory isn’t just steep — it’s structurally supported by government genomics funding and population-scale ambitions.

 

Latin America

Adoption here is sporadic but improving.

• Brazil is emerging as a regional leader. Academic centers are now using TGS in biodiversity genomics and cancer research.

• Mexico and Chile are piloting public health use cases, particularly for infectious disease outbreak response.

• Private labs are beginning to invest in nanopore platforms for clinical metagenomics and microbiome testing .

However, limited infrastructure and skilled workforce availability remain key adoption bottlenecks — especially in rural areas.

 

Middle East & Africa

This region is still in the early adoption phase , but several promising signals are emerging:

• The UAE and Saudi Arabia are funding personalized genomics programs that include TGS as a core technology — often through partnerships with U.S. and European biotech firms.

• In Africa , interest is growing in mobile sequencing units for outbreak monitoring (e.g., Ebola, malaria genotyping). Oxford Nanopore’s portable systems are seeing early traction here.

Training, logistics, and cost barriers are still significant, but international NGOs and academic collaborations are helping bridge the gap — particularly in East Africa.

 

End-User Dynamics And Use Case

The adoption of third generation sequencing (TGS) is no longer confined to academic institutions. What was once seen as an experimental platform is now getting built into core workflows across multiple end-user segments — from biotech companies to hospitals and even field-based public health labs.

Let’s break down how different stakeholders are putting TGS to work.

Academic and Research Institutions

This group laid the foundation for TGS adoption. Long-read sequencing is particularly valuable in basic science research because it enables:

• De novo genome assembly without reference bias

• Full-length transcript discovery

• Direct epigenetic modification detection (e.g., 5mC, 6mA)

• Study of repetitive and low-complexity regions

Many labs now use PacBio HiFi or Oxford Nanopore platforms for plant genomics, microbial ecology, developmental biology, and neurogenomics.

That said, adoption is still limited by budget in some public universities. However, consortium-based funding (e.g., NIH, EU Horizon grants) is helping maintain a steady baseline.

 

Pharmaceutical and Biotech Companies

Biopharma players are becoming major drivers of TGS demand , especially in drug discovery and biomarker development. Use cases include:

• Phasing of complex alleles in gene therapy candidates

• Structural variant mapping for CAR-T or monoclonal antibody pipelines

• Understanding transcript isoforms in oncology or neurology R&D

Some companies are integrating long-read transcriptomics into their screening platforms , particularly in CNS and immuno-oncology programs.

Also, TGS is proving valuable in pharmacogenomics — helping companies understand population-level differences in drug response.

Insight: “TGS gives us not just a sequence, but a functional readout. It’s helping us find variants we couldn’t even see with short-read.” — VP of Translational Research, Mid-sized Biotech (USA).

 

Clinical Diagnostic Laboratories

This is where TGS is showing some of its most exciting potential — and also its steepest regulatory hurdles.

Use cases:

• Rare disease diagnosis : Identifying structural variations, repeat expansions, or novel variants that were previously missed

• Cancer diagnostics : Detecting complex fusions, epigenetic signatures, and full-length transcripts

• Pre-implantation genetic screening : High-resolution structural variant detection in embryos

 

However, clinical adoption is still in early stages due to:

• Lack of widespread reimbursement frameworks

• Need for regulatory approvals

• Limited expertise in long-read bioinformatics

Still, early-mover labs — particularly in Europe and the U.S. — are running hybrid workflows (short-read + long-read) to validate difficult variants. Over time, TGS could reduce dependence on multi-assay diagnostic panels by offering a more comprehensive, single-pass readout.

 

Agricultural Genomics Facilities

TGS is playing an increasingly vital role in crop improvement and animal genomics . Use cases here include:

• Genotyping of elite breeding lines

• Detection of structural variants in livestock genomes

• Tracking of genetic diversity in wild populations

Because TGS provides better insight into gene duplications and transposable elements , it’s quickly replacing short-read systems for complex polyploid plants like wheat or sugarcane.

Governments in China, India, and Brazil are funding TGS-based agricultural R&D at scale.

 

Field-Based Use Case: Clinical Genomics in Neonatal ICU

A tertiary hospital in South Korea integrated Oxford Nanopore sequencing into its neonatal intensive care unit (NICU) to diagnose critically ill newborns with suspected genetic disorders.

Instead of sending out samples for exome sequencing (2–4 week turnaround), the hospital team used a portable nanopore sequencer onsite and ran real-time whole genome sequencing .

• Time to result: less than 8 hours

• Identified a rare structural variant in a mitochondrial gene

• Enabled targeted intervention within 24 hours

This use case reflects a broader trend: long-read platforms are shrinking the distance between sequencing and decision-making .

 

Summary by End User:

End User	Adoption Stage	Key Use Cases
Academic Institutions	Mature	De novo assembly, epigenetics, metagenomics
Pharma & Biotech	Expanding	Drug target validation, transcriptomics, pharmacogenomics
Clinical Labs	Emerging	Rare disease and oncology diagnostics
Agrigenomics Labs	Scaling	Trait selection, genome diversity mapping
Hospitals	Experimental	Neonatal genomics, real-time ER diagnostics

The big takeaway? The value of TGS isn’t theoretical anymore. It’s practical — and it's showing up exactly where speed, resolution, and functional interpretation matter most.

 

Recent Developments + Opportunities & Restraints

Recent activity in the third generation sequencing (TGS) market reflects a shift from core R&D to applied genomics — with companies, governments, and consortia investing in infrastructure, clinical studies, and hybrid workflows that bridge discovery and diagnostics.

Recent Developments

• PacBio launched Revio™ system upgrades in Q2 2024, enhancing throughput by 30% and reducing per-sample sequencing costs for high-volume users. It’s part of their broader push into national genome initiatives in Europe and Asia.

• Oxford Nanopore announced a new collaboration with the UK NHS focused on deploying real-time genomic surveillance tools in public hospitals — targeting sepsis and antimicrobial resistance with portable sequencers.

• QIAGEN expanded its bioinformatics cloud pipeline , adding real-time epigenome annotation modules in collaboration with leading cancer centers. This move aims to close the analysis gap in clinical-grade methylation datasets.

• China’s Ministry of Science and Technology launched a $120M genomics innovation fund, with a dedicated track for TGS technology localization. This includes reagent manufacturing, platform optimization, and domestic instrument scale-up.

• NIH-funded projects in the U.S. began incorporating TGS platforms into All of Us and Cancer Moonshot workflows — with a focus on underserved populations and structural variant detection.

These moves signal a turning point: the market is shifting from pure innovation to scale deployment.

 

Opportunities

• Clinical-Grade Structural Variant Profiling Long-read sequencing excels at detecting complex genomic events that short-read tools often miss. As payer frameworks evolve, particularly in rare disease and oncology, this capability may unlock reimbursement-driven growth.

• Multiomic Diagnostics The integration of DNA, RNA, and methylation data into single-assay workflows is creating a new diagnostics tier. TGS platforms that can detect base modifications directly — without conversion steps — are uniquely positioned to lead this transformation.

• Real-Time Outbreak Genomics As public health systems scale up genomic surveillance, the portability and speed of nanopore-based platforms provide a powerful toolset for pandemic preparedness, antimicrobial resistance, and emerging pathogen detection.

• Population Genomics in Developing Markets Asia Pacific, Latin America, and parts of Africa are accelerating genome programs. TGS technologies that offer affordability and low infrastructure dependency will benefit most in these settings.

• Drug Discovery & Functional Genomics Biopharma companies are using TGS in functional screening, cell-line characterization, and allele-specific expression analysis. This unlocks a new tier of preclinical decision-making, particularly for gene therapies and biologics.

 

Restraints

• High Capital and Operating Costs Despite falling reagent prices, the total cost of ownership for many TGS platforms — particularly SMRT systems — remains a hurdle for smaller labs. This limits penetration beyond elite research centers.

• Limited Clinical Validation Pipelines There’s still a gap between technical capability and regulatory-grade evidence. Many potential use cases (like structural variant panels or methylation diagnostics) are stuck in pilot stages due to lack of harmonized data standards and regulatory clarity.

• Bioinformatics Skill Bottleneck Handling TGS data requires specialized tools and expertise. Many hospitals and labs — especially in emerging regions — lack trained personnel for long-read-specific QC, variant calling, and annotation workflows.

• Vendor Lock-In and Workflow Rigidity Some platforms still require proprietary reagents and hardware, limiting flexibility in multi-vendor settings. This also slows down workflow innovation, particularly in hybrid labs using both short- and long-read systems.

• Reimbursement Lag Payers remain cautious. Despite strong academic evidence, few long-read assays have crossed into mainstream clinical reimbursement. That delay slows clinical adoption and investor confidence alike.

Bottom line? The market is moving — but its trajectory depends on one thing: execution. For TGS to reach its full potential, it’s not just about better hardware or more data. It’s about translating those capabilities into clinical-grade performance, at scale, and at price points that global systems can support.

 

7.1. Report Coverage Table

Report Attribute	Details
Forecast Period	2024 – 2030
Market Size Value in 2024	USD 2.1 Billion
Revenue Forecast in 2030	USD 5.8 Billion
Overall Growth Rate	CAGR of 18.5% (2024 – 2030)
Base Year for Estimation	2024
Historical Data	2019– 2023
Units	USD Million, CAGR (2024 – 2030)
Segmentation	By Technology, By Application, By End User, By Geography
By Technology	Single Molecule Real-Time (SMRT) Sequencing, Nanopore Sequencing
By Application	Genomics & Epigenomics, Transcriptomics, Oncology, Infectious Disease Diagnostics, Rare Disease Detection, Agrigenomics, Neurodegenerative Research
By End User	Academic & Research Institutions, Pharmaceutical & Biotech Companies, Clinical Diagnostics Laboratories, Agricultural Genomics Facilities
By Region	North America, Europe, Asia Pacific, Latin America, Middle East & Africa
Country Scope	U.S., Canada, Germany, U.K., China, Japan, India, Brazil, South Korea, GCC
Market Drivers	- High demand for accurate structural variant detection - Growing clinical applications in oncology and rare diseases - Increasing accessibility of portable, real-time sequencing platforms
Customization Option	Available upon request