Illumina sequencing platforms

Our innovative next-generation sequencing (NGS) platforms deliver exceptional data quality and accuracy, at a massive scale. View benchtop and production-scale sequencer comparison tables, and find tools designed to help you choose the right platform for your needs.

Sequencing Platforms

 
iSeq 100
MiniSeq
MiSeq Series
NextSeq 550 Series
NextSeq 1000 & 2000
Popular Applications & Methods
Key Application Key Application Key Application Key Application Key Application
Large Whole-Genome Sequencing (human, plant, animal)          
Small Whole-Genome Sequencing (microbe, virus)          
Exome & Large Panel Sequencing (enrichment-based)          
Targeted Gene Sequencing (amplicon-based, gene panel)          
Single-Cell Profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays)          
Transcriptome Sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)          
Targeted Gene Expression Profiling          
miRNA & Small RNA Analysis          
DNA-Protein Interaction Analysis (ChIP-Seq)          
Methylation Sequencing          
16S Metagenomic Sequencing          
Metagenomic Profiling (shotgun metagenomics, metatranscriptomics)          
Cell-Free Sequencing & Liquid Biopsy Analysis          
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Run Time 9.5–19 hrs 4–24 hours 4–55 hours 12–30 hours 8–44 hours
Maximum Output 1.2 Gb 7.5 Gb 15 Gb 120 Gb 540 Gb *
Maximum Reads Per Run 4 million 25 million 25 million 400 million 1.8 billion *
Maximum Read Length 2 × 150 bp 2 × 150 bp 2 × 300 bp 2 × 150 bp 2 × 300 bp
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NextSeq 1000 & 2000
NovaSeq 6000 Series
NovaSeq X Series
Popular Applications & Methods
Key Application Key Application Key Application
Large Whole-Genome Sequencing (human, plant, animal)      
Small Whole-Genome Sequencing (microbe, virus)      
Exome & Large Panel Sequencing (enrichment-based)      
Targeted Gene Sequencing (amplicon-based, gene panel)      
Single-Cell Profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays)      
Transcriptome Sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)      
Chromatin Analysis (ATAC-Seq, ChIP-Seq)      
Methylation Sequencing      
Metagenomic Profiling (shotgun metagenomics, metatranscriptomics)      
Cell-Free Sequencing & Liquid Biopsy Analysis      
See what's possible with the NovaSeq X series

Larger projects, deeper sequencing, faster than ever. Breakthrough innovations for groundbreaking discoveries.

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Run Time 8–44 hours ~13–38 hours (dual SP flow cells)
~13–25 hours (dual S1 flow cells)
~16–36 hours (dual S2 flow cells)
~44 hours (dual S4 flow cells)
~15–21 hours (1.5B flow cells)
~18–25 hours (10B flow cells)
~48 hours (25B flow cells)
Maximum Output 540 Gb * 6000 Gb 16 Tb
Maximum Reads Per Run 1.8 billion * 20 billion 26 billion (single flow cells)
52 billion (dual flow cells)
Maximum Read Length 2 × 300 bp 2 x 250 bp** 2 × 150 bp
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* Specifications based on Illumina PhiX control library at supported cluster densities.
** Specification based on dual flow cell run of SP flow cells.
† For MiSeq V3 kits only.

When determining the best sequencing platform for your lab, you’ll want to ask the right questions to evaluate your needs. These include:

  • What applications will you use most frequently?
  • Which instrument options best enable these applications?
  • What are the ongoing costs beyond initial instrument purchase?

Use this checklist as a framework. For detailed insight on the factors to consider in each area, download the full NGS System Buyer’s Guide.

Download Buyer’s Guide

NGS Platforms with Proven Performance

Illumina NGS instruments have been adopted by leading institutions around the globe, both big and small, and are the production platform for many genome centers. Illumina NGS technology is cited in over 300,000 peer-reviewed publications—5× more than all other NGS technologies combined*

Each sequencing platform delivers exceptional data quality and performance, with flexible throughput and simple, streamlined workflows—for every kind of researcher, for every scale of study.

*Data calculations on file, Illumina, Inc. 2022.

Illumina has pioneered major advances in sequencing simplicity, flexibility, and platform performance. Sequencing output has grown over ten thousand-fold, from less than 1 gigabase to 16 terabases per run, while the number of reads has increased from millions to tens of billions. Experiments that once required complex workflows now use simple push-button sequencing.

Learn More About NGS

Find the Right NGS Platform

Use our interactive comparison tool to identify the best sequencing instrument for your lab and applications. This tool will help you compare next-generation sequencing systems and find the one that's right for your lab or application. You can email the results or request a consultation.

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