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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 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          
Benchtop Sequencer Sheds Light on Ebola Outbreak

Local scientists use the iSeq 100 Sequencing System to analyze transmission patterns and trace the origin of an Ebola outbreak in the Democratic Republic of the Congo.

Read Article
Run Time 9.5–19 hrs 4–24 hours 4–55 hours 12–30 hours 24-48 hours
Maximum Output 1.2 Gb 7.5 Gb 15 Gb 120 Gb 300 Gb*
Maximum Reads Per Run 4 million 25 million 25 million † 400 million 1 billion*
Maximum Read Length 2 × 150 bp 2 × 150 bp 2 × 300 bp 2 × 150 bp 2 × 150 bp
 
Explore iSeq 100
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Explore MiniSeq
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Compare MiSeq
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Compare NextSeq 550
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Explore NextSeq 2000
 
NextSeq 550 Series
NextSeq 2000
NovaSeq 6000
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      
Optimized NGS Sample Tracking and Workflows

See how a Laboratory Information Management System (LIMS) enabled this large genomics lab to standardize lab procedures and cope with increasing sample volumes from diverse clients.

Read Case Study
Run Time 12–30 hours 24-48 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)
Maximum Output 120 Gb 300 Gb* 6000 Gb
Maximum Reads Per Run 400 million 1 billion* 20 billion
Maximum Read Length 2 × 150 bp 2 × 150 bp 2 x 250**
 
Compare NextSeq 550
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Explore NextSeq 2000
 
Explore NovaSeq 6000
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* Maximum specs available with the NextSeq 2000 P3 Reagents, available late 2020; specifications subject to change.
** Specification based on dual flow cell run of SP flow cells.
† For MiSeq V3 kits only.

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Find the Right NGS Platform

Use our interactive comparison tool to identify the best sequencing instrument for your lab and applications.

Launch Comparison Tool

See all product selection and experiment planning tools

Next-Generation Sequencing Platform Innovation is in our DNA

Illumina has pioneered major advances in sequencing simplicity, flexibility, and platform performance. Sequencing output has grown over a thousand-fold, from less than 1 gigabase to 6 terabases per run, while the number of reads has increased from millions to billions. Experiments that once required complex workflows now use simple push-button sequencing.

Learn More About NGS
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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. More than 90% of the world’s sequencing data is generated using Illumina instruments.*

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. 2015.

How to Choose a Sequencer

Determine the best benchtop or production-scale sequencing platform to transform your lab. Ask the right questions to evaluate your needs.

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

For further guidance about key factors to consider when making your decision, download the NGS System Buyer’s Guide.

Download Buyer's Guide

Do you own a MiniSeq System?

There is a MiniSeq Software System Suite upgrade available. Complete the form to schedule an upgrade and receive several enhancements including a Windows 10 operating system upgrade and feature updates to Local Run Manager Software.