Short-Read Sequencing Market - Global Industry Size, Share, Trends, Opportunity, and Forecast, Segmented By Product (Instruments, Consumables, Services), By Application (Whole Genome Sequencing, Whole Exome Sequencing, Targeted Sequencing & Resequencing, Others), By End User (Academic & Research Institutes, Hospitals & Clinics, Pharmaceutical & Biotechnology Companies, Others), By Region and Competition, 2021-2031F

Forecast Period	2027-2031
Market Size (2025)	USD 7.03 Billion
CAGR (2026-2031)	8.35%
Fastest Growing Segment	Consumables
Largest Market	North America
Market Size (2031)	USD 11.37 Billion

Market Overview

The Global Short-Read Sequencing Market will grow from USD 7.03 Billion in 2025 to USD 11.37 Billion by 2031 at a 8.35% CAGR. Short-read sequencing is a high-throughput genomic analysis methodology that generates DNA reads typically ranging from 75 to 300 base pairs to identify genetic variants with exceptional accuracy. The expansion of this market is primarily supported by the precipitous decline in sequencing costs and the deepening integration of genomic data into clinical workflows for oncology and rare disease diagnostics. This growing reliance on genomic profiling for treatment selection is evidenced by recent regulatory trends; according to the Personalized Medicine Coalition, in 2024, personalized medicines accounted for approximately 38 percent of new therapeutic molecular entities approved by the Food and Drug Administration.

Despite these favorable growth factors, the sector faces a significant impediment regarding the management and interpretation of the massive datasets generated by modern sequencing platforms. The substantial computational infrastructure required to process, store, and analyze these vast volumes of genomic information creates a bioinformatic bottleneck that complicates the rapid translation of raw data into actionable clinical insights and limits broader adoption in resource-constrained environments.

Key Market Drivers

The continuous decline in sequencing costs and per-gigabase expenses serves as a primary catalyst for the Global Short-Read Sequencing Market, effectively democratizing access to high-throughput genomic data. This downward pricing trajectory is driven by fierce competition among platform developers and the introduction of ultra-high-throughput systems that significantly reduce the financial barrier for whole-genome analysis. Such economic efficiency allows research institutions and clinical laboratories to transition from targeted panels to comprehensive whole-genome sequencing (WGS) without increasing their budgets. According to Frontline Genomics, March 2025, in the 'The $100 Genome: Where's the Limit?' article, Ultima Genomics announced the achievement of the $80 genome, a price point that substantially undercuts historical industry benchmarks and accelerates the feasibility of routine clinical sequencing.

Simultaneously, the implementation of large-scale population genomics programs is generating unprecedented demand for short-read sequencing capacity as nations strive to characterize genetic diversity and disease susceptibility at a population level. These massive initiatives require robust short-read platforms to process hundreds of thousands of samples with high accuracy and speed. According to the National Institutes of Health, February 2025, in the 'All of Us Adds Data from 50% More Participants' announcement, the All of Us Research Program expanded its genomic dataset to include whole genome sequences from more than 414,000 participants. This surge in high-volume sequencing activity directly translates into substantial industrial revenue; according to Illumina, October 2025, in the 'Illumina Reports Financial Results for Third Quarter of Fiscal Year 2025', the company reported revenue of $1.08 billion for the quarter, highlighting the sustained commercial impact of these large-scale genomic demands.

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Key Market Challenges

The management and interpretation of massive datasets, often referred to as the bioinformatic bottleneck, stands as a critical challenge hampering the growth of the Global Short-Read Sequencing Market. While the physical process of generating genomic reads has achieved high throughput at lower costs, the downstream computational analysis remains disproportionately expensive and technically demanding. This disparity creates a workflow paralysis where data production outpaces the capacity to process and interpret the information, effectively delaying the translation of raw DNA sequences into actionable clinical reports. Laboratories lacking substantial computational infrastructure struggle to handle this data deluge, which restricts the technology's expansion into community hospitals and resource-constrained settings.

This complexity in data handling creates a severe operational barrier that deters potential adopters who cannot afford the necessary specialized IT resources. The difficulty lies not only in storage volume but also in the usability of the generated information. According to the Pistoia Alliance, in 2024, 54 percent of life science professionals cited unstructured data as a primary barrier to utilizing experimental findings effectively. As a result, the market experiences friction as the high indirect costs associated with data curation and bioinformatic analysis discourage the broader integration of short-read sequencing into standard diagnostic procedures.

Key Market Trends

The proliferation of liquid biopsy for non-invasive oncology is fundamentally altering the demand landscape for short-read sequencing by shifting clinical focus from tissue-based diagnostics to blood-based genomic profiling. This trend is driven by the increasing utility of circulating tumor DNA (ctDNA) analysis for therapy selection and minimal residual disease (MRD) monitoring, which requires deep sequencing coverage to detect low-frequency variants with high sensitivity. Unlike traditional biopsies, these non-invasive assays allow for frequent longitudinal monitoring of tumor evolution, thereby creating a sustained stream of sequencing throughput requirements for clinical laboratories. The commercial impact of this shift is evident in the rapid scaling of diagnostic providers; according to Guardant Health, February 2025, in the 'Fourth Quarter and Full Year 2024 Financial Results' report, the company reported a 31 percent year-over-year increase in total revenue to $739 million, supported by a 20 percent growth in clinical oncology test volumes.

Simultaneously, the market is expanding into spatial genomics and multi-omics integration, moving beyond bulk DNA analysis to capture the complex interplay between genomic architecture and cellular organization. This trend involves the convergence of next-generation sequencing with high-resolution imaging and protein analysis, allowing researchers to map gene expression and cellular phenotypes within their native tissue context. This integration is particularly critical for understanding tumor microenvironments and immune responses, necessitating advanced platforms that can simultaneously process genomic and proteomic data. Innovators are rapidly deploying systems to meet this complex demand; according to Element Biosciences, July 2025, in the 'Element Biosciences Surpasses 50 AVITI24 5D Multiomic System Installations' press release, the company announced that it had installed over 50 units of its flagship integrated multiomic platform globally within just seven months of its commercial launch.

Segmental Insights

The Consumables segment is identified as the fastest-growing category within the Global Short-Read Sequencing Market due to the recurring necessity for reagents and library preparation kits. Unlike capital equipment which involves a singular investment, consumables are required for every individual sequencing run, directly linking revenue growth to the increasing volume of genomic testing. This expansion is further supported by the rising adoption of sequencing for clinical diagnostics, which demands a consistent supply of validated test materials. Consequently, this repetitive purchasing model ensures that consumables sustain a higher growth trajectory compared to instruments and services.

Regional Insights

North America maintains a leading position in the global short-read sequencing market, driven by substantial investments in genomic research and a high concentration of key biotechnology firms. The region's dominance is supported by extensive funding from institutions such as the National Institutes of Health, which fosters continuous development in clinical diagnostics and personalized medicine. Furthermore, the U.S. Food and Drug Administration provides a structured regulatory pathway that encourages the commercial adoption of sequencing technologies. This combination of capital investment, institutional support, and regulatory clarity ensures North America remains the primary hub for market expansion.

Recent Developments

• In October 2024, Illumina unveiled the MiSeq i100 Series, a new line of benchtop systems designed to deliver enhanced speed and simplicity for the short-read sequencing market. The series introduced XLEAP-SBS chemistry to a compact form factor, enabling room-temperature storage and shipping of reagents, which significantly improves logistical flexibility for laboratories. These instruments were engineered to provide run times as fast as four hours, allowing for same-day sample-to-analysis results that accelerate decision-making in critical research areas. The launch addressed the market's growing demand for affordable, plug-and-play sequencing solutions that require minimal bioinformatic expertise while maintaining high data quality.
• In June 2024, MGI Tech announced a strategic collaboration with SeqOne to advance end-to-end genomic analysis solutions tailored for human genetics and pathology laboratories. This partnership focused on validating workflows that integrate MGI’s DNBSEQ short-read sequencing platforms with SeqOne’s AI-driven analytical tools to streamline diagnostic processes. The initiative included the validation of an automated solution for homologous recombination deficiency signatures and the compatibility of tertiary analysis software with MGI’s bioinformatics acceleration hardware. The cooperation aimed to deliver cost-effective, high-precision diagnostic workflows that enhance the efficiency of variant identification and reporting for clinical researchers worldwide.
• In April 2024, Element Biosciences announced the commercial availability of the AVITI24 system, an innovative instrument that integrates state-of-the-art short-read sequencing with cyto-profiling capabilities. This platform enables researchers to simultaneously examine DNA, RNA, proteins, and cell structure within single cells, significantly expanding the utility of benchtop sequencing for complex biological analysis. Powered by the company's proprietary Teton chemistry, the system simplifies multi-omics workflows by providing a unified readout in less than 24 hours. The launch was positioned to support advanced applications in cancer research and drug development, allowing for the direct profiling of up to one million cells per experiment to uncover molecular interactions.
• In January 2024, Ultima Genomics announced the full commercial availability of its UG 100 sequencing system, marking a significant milestone in the high-throughput short-read sequencing sector. The platform utilizes a novel open silicon wafer architecture designed to replace traditional flow cells, thereby enabling massive scalability and lower costs for genomic data generation. The system integrates the company's ppmSeq technology, which ensures high raw read accuracy for demanding applications such as single nucleotide variant calling and rare event detection. This launch followed an extensive early access program involving partnerships with leading genome centers to mature the technology for broad clinical and research adoption.

Key Market Players

• Illumina, Inc.
• Invitae Corporation
• Thermo Fisher Scientific, Inc.
• Pacific Biosciences of California, Inc.
• BGI Genomics Co., Ltd
• QIAGEN NV
• Agilent Technologies, Inc.
• Azenta US, Inc.
• PerkinElmer, Inc.
• ProPhase Labs, Inc.

By Product	By Application	By End User	By Region
Instruments Consumables Services	Whole Genome Sequencing Whole Exome Sequencing Targeted Sequencing & Resequencing Others	Academic & Research Institutes Hospitals & Clinics Pharmaceutical & Biotechnology Companies Others	North America Europe Asia Pacific South America Middle East & Africa

Report Scope:

In this report, the Global Short-Read Sequencing Market has been segmented into the following categories, in addition to the industry trends which have also been detailed below:

• Short-Read Sequencing Market, By Product:

• Instruments
• Consumables
• Services

• Short-Read Sequencing Market, By Application:

• Whole Genome Sequencing
• Whole Exome Sequencing
• Targeted Sequencing & Resequencing
• Others

• Short-Read Sequencing Market, By End User:

• Academic & Research Institutes
• Hospitals & Clinics
• Pharmaceutical & Biotechnology Companies
• Others

• Short-Read Sequencing Market, By Region:

• North America
• United States
• Canada
• Mexico
• Europe
• France
• United Kingdom
• Italy
• Germany
• Spain
• Asia Pacific
• China
• India
• Japan
• Australia
• South Korea
• South America
• Brazil
• Argentina
• Colombia
• Middle East & Africa
• South Africa
• Saudi Arabia
• UAE