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Illumina innovation roadmap

Our technology innovation and product development roadmap is designed to enable researchers and clinicians to turn big dreams into impactful genomic discoveries, improving lives and changing the course of diseases globally

Illumina product development roadmap

Our innovation roadmap is part of a proven track record of biological solutions that empower researchers to perform studies at the throughput, scale, and price that meets their research objectives.

We highlight upcoming technologies here that are being developed into future products, with a focus on ease-of-use and sustainability. Illumina keenly pursues innovation by prioritizing internal research and development in our roadmap, continually competing against ourselves to create even better products.

Explore current innovations

Constellation mapped reads

Estimated availability*: 1H 2026

Constellation mapped read technology uses a highly simplified NGS workflow that enables on-flow cell library prep with standard short-reads with cluster proximity information.

This innovative method eliminates standard library prep and unlocks long-distance genomic information. Early testing demonstrates enhanced mapping of challenging genomic regions, ultra-long phasing (Mb), and improved detection of large structural rearrangements.

2024 Illumina Innovation Roadmap

Hear how Illumina innovations in library prep, sequencing, and analysis, including mapped reads, are enabling transformative applications using multiomics, plus get customer insights into early testing of constellation mapped read technology for human whole-genome sequencing.

View webinar

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FAQ

Illumina constellation mapped read technology is currently being developed for the NovaSeq X Series and demonstrated compatible with benchtop platforms. Analysis will utilize DRAGEN pipeline and be compatible with the Illumina WGS tertiary analysis solution.

The constellation workflow begins with a novel, on-flow-cell library prep that uses the low DNA inputs characteristic of transposome-based library prep workflows and the high sequencing quality of the NovaSeq X Series. The experimental workflow requires no modifications to the sequencing instrument—only a custom sequencing recipe, making it readily accessible to researchers.

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Spatial transcriptomics

Estimated availability*: 1H 2026

Illumina spatial technology will enable a unique end-to-end spatial transcriptomics solution for use with Illumina high-throughput sequencing systems.

Illumina spatial technology captures poly(A) motifs of RNA transcripts on an advanced substrate for hypothesis-free analysis of gene expression profiling. This design also allows easy application of the technology across any eukaryotic species.

Streamlined and powerful data analysis is being developed for Illumina Connected Multiomics powered by DRAGEN analysis. The complete workflow will offer image integration, machine-learning analysis tools, access to a purpose-built spatial browser for visualizations, future multiomic integration, and data management.

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Introducing Illumina spatial technology

Building on our expertise in flow cell surface development and manufacturing, Illumina spatial technology will provide highly sensitive whole-transcriptome coverage with unprecedented resolution, giving researchers clarity without compromises.

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FAQ

Illumina spatial technology utilizes a large, advanced tissue placement area with continuous 1µm surface features. The captured transcripts are binned with integrated cell segmentation through the Illumina spatial analysis pipeline.

During development, we have seen that coverage varies based on tissue type, tissue quality, and sequencing depth. We have observed that the technology can detect over 200% more genes in a tissue section compared to other spatial solutions.1

The initial version of Illumina spatial technology is optimized for use with fresh-frozen tissue. A version supporting formalin-fixed paraffin-embedded (FFPE) tissue is in development.

Due to the required depth of sequencing, we recommend the NovaSeq X Series or NovaSeq 6000 System. The NextSeq 2000 System may be used for smaller tissue sections or tissue arrays.

Two versions will be available: a large-format slide with a 50 x 15 mm capture area and a second format with a smaller capture area. Both versions will use a standard 75 × 25 mm microscope slide.

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5-base solution for methylation studies

Estimated availability*: 2H 2025

The Illumina 5-base solution will deliver simultaneous high-accuracy genomic and epigenomic discovery in a single readout.

Novel chemistry converts 5-methylcytosine (5mC) to thymine (T) in a simple, single step. The streamlined workflow includes optimized library prep that’s complete in less than a day and easy-to-use analysis for dual genomic and epigenomic annotations and visualizations.

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Illumina 5-base solution

This solution measures DNA methylation and genetic variation together, with exceptional accuracy, simplicity, and scale.

Flyer published: Feb. 24th, 2025

Epigenetics education

Explore specific techniques to study epigenetic modifications such as methylation patterns, DNA–protein interactions, and chromatin analysis.

FAQ

The 5-base solution uses a combination of Illumina proprietary innovations, including novel conversion chemistry and cutting-edge algorithms, to provide accurate genetic variant and methylation detection in a single, easy-to-use assay.

While conventional methylation conversion technologies convert unmethylated cytosine to thymine, Illumina proprietary conversion chemistry selectively converts methylated cytosine to thymine. As the majority of cytosines in a healthy human genome are unmethylated, selective conversion of methylated cytosine produces higher complexity libraries and, when combined with novel informatics, provides comprehensive, cost-effective 5-base insights.

  • 5-base insights: Accurate genetic variant and methylation detection in a single assay.
  • Simplicity: Single-step conversion and library prep completed in a single day.
  • Flexibility: Compatible with different sample types and methods, including PCR+, enrichment, and PCR-Free.
  • Affordability: Efficient sequencing for 5-base insights.
  • Seamless solution from single provider: Illumina library prep-through-analysis solution and support.

The solution will be scalable on Illumina mid- to high-throughput sequencing platforms: the NextSeq 2000 System and NovaSeq X Series.

The bioinformatics solution does not require advanced expertise. It offers highly accurate variant and methylation detection. This is a simple, powerful, and easy-to-use multiomic analysis solution. Insights from Illumina Connected Multiomics are powered by DRAGEN analysis.

/ Results

Multiomic data analysis for biologists

Estimated availability*: 2H 2025

Illumina Connected Multiomics is a fully integrated multiomic analysis software solution that will enable seamless sample-to-insights workflows.

With intuitive and scalable multiomic analysis, it empowers researchers to leverage powerful statistics and interactive visualizations to unlock deeper biological insights. Illumina Connected Multiomics integrates datasets from genomics, spatial transcriptomics, proteomics, and more with out-of-the-box workflows to support Illumina multiomic library prep kits.

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Streamlined and powerful spatial data analysis

Illumina Connected Multiomics, with DRAGEN analysis, will offer streamlined and powerful multiomic visualization and insights. The workflow will offer image integration, machine-learning analysis tools, access to a spatial browser for visualizations, future multiomic integration, and data management.

In addition to spatial transcriptomics, Connected Multiomics supports other data types including single cell, protein, and more.

Related resources

Multiomics education

Use multiomics profiling to multiply discovery power and better connect genotype to phenotype.

Multiomics multiplies your discovery power

See how you can use multiomics to better connect genotype to phenotype and obtain a full cellular readout not found through single omics approaches.

Recently launched innovation products

Explore examples of innovative Illumina products that were developed and launched recently.

Illumina Single Cell 3' RNA Prep

Accessible and highly scalable single-cell RNA-Seq solution for mRNA capture, barcoding, and library prep without complex workflows or microfluidics

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*Product availability estimates are rough timing estimates that are subject to change.

References
  1. Data on file. Illumina, Inc. 2025.