Sequencing platforms

Trusted technology and proven performance empower scientists to explore further, with confidence. View production-scale and benchtop sequencers, compare features, and learn how to choose the right next-generation sequencing (NGS) platform for your needs.

NovaSeq X Plus dual sequencing touch screen monitor,

Production-scale sequencers

Key specifications

NextSeq 1000 and 2000 Systems


NovaSeq 6000 System

NovaSeq X Series

Max output per flow cell 540 Gba 3 Tbb 8 Tbc
Run time (range)d ~8–44 hr ~13–44 hr ~17–48 hr
Max reads per run (single reads) 1.8Ba

10B (single flow cell)b

20B (dual flow cells)b

26B (single flow cell)c

52B (dual flow cells)c,e

Max read length 2 × 300 bp 2 × 250 bp 2 × 150 bp
Key applications and methodsf      

Large whole-genome sequencing

(human, plant, animal)

 
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Small whole-genome sequencing

(microbe, virus)

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Exome and large panel sequencing

(enrichment-based)

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Targeted gene sequencing

(amplicon-based, gene panel)

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Single-cell profiling

(scRNA-Seq, scDNA-Seq, oligo tagging assays)

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Transcriptome sequencing

(total RNA-Seq, mRNA-Seq, gene expression profiling)

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Chromatin analysis

(ATAC-Seq, ChIP-Seq)

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Methylation sequencing

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Metagenomic profiling

(shotgun metagenomics, metatranscriptomics)

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Cell-free sequencing & liquid biopsy analysis

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Explore NextSeq 1000 and 2000 Systems

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Explore NovaSeq 6000 System

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Explore NovaSeq X Series

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a. Specifications based on a single flow cell run of P4 flow cell using Illumina PhiX control library at supported cluster densities. P4 flow cells are available for the NextSeq 2000 System only. 

b. Specifications based on a single flow cell run of S4 flow cell using Illumina PhiX control library at supported cluster densities.

c. Specifications based on Illumina PhiX control library, or a TruSeq DNA Library created with NA12878 at supported cluster densities. Performance may vary based on library type and quality, insert size, loading concentration, and other experimental factors.

d. Run times includes cluster generation, sequencing, and base calling on a NextSeq 1000 or NextSeq 2000 System and NovaSeq 6000 System. Run times include automated onboard cluster generation, sequencing, automated post-run wash, and base calling on the NovaSeq X Systems.

e. Dual flow cell runs only apply to the NovaSeq X Plus System.

f. Checkmark indicates an application or method optimized for the sequencing system.

Benchtop sequencers

Benchtop sequencers offer flexibility and operational simplicity. Looking for information to determine if these platforms are well-suited to your needs, and guidance selecting the right one?

Key specifications

iSeq 100 System

MiniSeq System

MiSeq System

NextSeq 550 System

NextSeq 1000 and 2000 Systems

Max output per flow cell 1.2 Gba 7.5 Gbb 15 Gbc 120 Gbb 540 Gbd
Run time (range)e ~9.5–19 hr ~5–24 hr ~5–56 hr ~11–29 hr ~8–44 hr
Max reads per run (single reads) 4Ma 25Mb 25Mc 400Mb 1.8Bd
Max read length 2 × 150 bp 2 × 150 bp 2 × 300 bp 2 × 150 bp 2 × 300 bp
Key applications and methodsf          

Large whole-genome sequencing

(human, plant, animal)

         

Small whole-genome sequencing

(microbe, virus)

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Exome & large panel sequencing

(enrichment-based)

     
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Targeted gene sequencing

(amplicon-based, gene panel)

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Single-cell profiling

(scRNA-Seq, scDNA-Seq, oligo tagging assays)

     
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Transcriptome sequencing

(total RNA-Seq, mRNA-Seq, gene expression profiling)

     
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Targeted gene expression profiling

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miRNA & small RNA analysis

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DNA-protein interaction analysis (ChIP-Seq)

   
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Methylation sequencing

     
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16S metagenomic sequencing

 
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Metagenomic profiling (shotgun metagenomics, metatranscriptomics)

     
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Cell-free sequencing & liquid biopsy analysis

     
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Explore iSeq 100 System

Order

Explore MiniSeq System

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Explore MiSeq System

Order

Explore NextSeq 550 System

Order

Explore NextSeq 1000 and 2000 Systems

Order

a. Specifications are based on the iSeq 100 i1 Reagents v2 (300 cycle) kit using Illumina PhiX control library at supported cluster densities. 

b. Specifications are based on a single flow cell run of the high-output flow cell using Illumina PhiX control library at supported cluster densities. MiniSeq and NextSeq 550 Systems use different high-output flow cells.

c. Specifications are based on a single flow cell run of the v3 flow cell using Illumina PhiX control library at supported cluster densities. 

d. Specifications based on a single flow cell run of the P4 flow cell using Illumina PhiX control library at supported cluster densities. P4 flow cells are available for the NextSeq 2000 System only.

e. Run times includes cluster generation, sequencing, base calling, and quality scoring.

f. Checkmark indicates an application or method optimized for the sequencing system.

NGS platforms for a growing sequencing community

Innovative NGS platforms with proven performance and exceptional customer support expand the genomics community on a global scale. With more than 15 Illumina Solutions Centers worldwide, over 600 support personnel, 24/5 remote technical support, onsite training, instrument qualification services, and customized onboarding solutions, Illumina provides researchers with the tools and support they need to be successful in their lab.

Scientist single pipetting into plate, sample tubes in the background

How to choose an NGS platform

Find the right sequencing instrument by exploring important considerations for every lab. 

Methods

Which library prep and sequencing methods will you perform for your desired applications? What are your throughput needs?

Software needs

What are your goals for automating your workflow, from lab management through analysis and interpretation? Are you looking for streamlined comprehensive informatics?

Technology and support

Will you benefit from application flexibility, expert-level technical support, and a global community of scientists?

Scientist single pipetting into plate, sample tubes in the background

A step-by-step guide to choosing an NGS platform

This comprehensive guide will walk you through the decision process by helping you evaluate your research goals and laboratory needs.

  • Key questions to ask before purchasing a sequencing platform
  • NGS instrument categories with key factors to consider
  • Considerations around applications and data analysis
  • NGS buyer’s checklist

Purchasing solutions

Get up and running quickly with a rental or leasing program designed to work with your budget. Explore ecommerce and purchasing solutions for your business needs.

Interested in an instrument demo or in speaking with someone?

Get a demo of the instrument that you are interested in or contact a specialist to get your questions answered. Fill out a request form and we will be in touch shortly.