Short-Read Sequencing Market - Global Industry Size, Share, Trends, Opportunity, and Forecast, 2021-2031

The Global Short-Read Sequencing Market is projected to expand from USD 7.03 Billion in 2025 to USD 11.37 Billion by 2031, reflecting a CAGR of 8.35%. This high-throughput methodology, which produces DNA reads typically between 75 and 300 base pairs, is prized for its ability to identify genetic variants with exceptional accuracy. Growth in this sector is primarily fueled by the precipitous decline in sequencing costs and the deepening integration of genomic data into clinical workflows for oncology and rare disease diagnostics. Recent regulatory trends underscore this increasing reliance on genomic profiling for treatment selection; for instance, the Personalized Medicine Coalition reported that personalized medicines comprised approximately 38 percent of new therapeutic molecular entities approved by the Food and Drug Administration in 2024.

Despite these positive growth drivers, the industry faces a significant impediment regarding the management and interpretation of the massive datasets produced by modern sequencing platforms. The extensive computational infrastructure needed to process, store, and analyze these vast volumes of genomic information creates a bioinformatic bottleneck. This issue complicates the rapid translation of raw data into actionable clinical insights and limits the technology's broader adoption in environments constrained by limited resources.

Market Drivers

The persistent decline in sequencing costs and per-gigabase expenses acts 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 clinical laboratories and research institutions to transition from targeted panels to comprehensive whole-genome sequencing (WGS) without increasing their budgets. Highlighting this trend, Frontline Genomics reported in a March 2025 article titled 'The $100 Genome: Where's the Limit?' that Ultima Genomics achieved an $80 genome, a price point that substantially undercuts historical benchmarks and accelerates the feasibility of routine clinical sequencing.

Concurrent with these cost reductions, the implementation of large-scale population genomics programs is generating unprecedented demand for short-read sequencing capacity as nations aim to characterize disease susceptibility and genetic diversity at a population level. These massive initiatives require robust platforms capable of processing hundreds of thousands of samples with high speed and accuracy. For example, the National Institutes of Health announced in February 2025 that the All of Us Research Program had expanded its genomic dataset to include whole genome sequences from over 414,000 participants. This surge in high-volume sequencing activity directly translates into substantial industrial revenue, as evidenced by Illumina's October 2025 financial report, which announced quarterly revenue of $1.08 billion, underscoring the sustained commercial impact of these large-scale genomic demands.

Market Challenges

The management and interpretation of massive datasets, often termed the bioinformatic bottleneck, stands as a critical challenge inhibiting the growth of the Global Short-Read Sequencing Market. While the physical process of generating genomic reads has achieved high throughput at lower costs, 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. Consequently, laboratories lacking substantial computational infrastructure struggle to handle this influx of data, 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, 54 percent of life science professionals in 2024 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.

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; for instance, Guardant Health reported a 31 percent year-over-year revenue increase to $739 million in February 2025, 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; for example, Element Biosciences announced in July 2025 that it had installed over 50 units of its flagship AVITI24 5D Multiomic System globally within just seven months of its commercial launch.

Key Players Profiled in the Short-Read Sequencing Market

• 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.

Report Scope

In this report, the Global Short-Read Sequencing Market has been segmented into the following categories:

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
• Europe
• Asia-Pacific
• South America
• Middle East & Africa

Competitive Landscape

Company Profiles: Detailed analysis of the major companies present in the Global Short-Read Sequencing Market.

Available Customization

The analyst offers customization according to your specific needs. The following customization options are available for the report:

• Detailed analysis and profiling of additional market players (up to five).

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