Instruments

Sequencing platforms

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

MiSeq i100 benchtop sequencer

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?

Learn how to choose a benchtop sequencer
 

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MiSeq i100 Series system render

NextSeq 550 System render

NextSeq 1000 and 2000 System render
Key specifications

MiSeq i100 Series

NextSeq 550 System

NextSeq 1000 and 2000 Systems
Max output per flow cell 30 Gb a 120 Gb b 540 Gb
Run time (range)c ~4–24 hr ~11–29 hr ~8–44 hr
Max reads per run (single reads) 100M a 400M b 1.8B
Max read length 2 × 500 bp 2 × 150 bp 2 × 300 bp
Key NGS applications and methodsd

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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Targeted gene expression profiling
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miRNA and 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 and liquid biopsy analysis
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Explore MiSeq i100 Series

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Explore NextSeq 550 System

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Explore NextSeq 1000 and 2000 Systems

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  1. Max range based on 100M flow cell specifications. 100M flow cells are available for the MiSeq i100 Plus System only.
  2. Specifications are based on a single flow cell run of the high-output flow cell using Illumina PhiX control library at supported cluster densities. NextSeq 550 Systems use different high-output flow cells.
  3. Run times includes cluster generation, sequencing, base calling, and quality scoring. Performance at the higher range of output specification is not guaranteed. Actual output is dependent on library type, user optimization, and run performance.
  4. Checkmark indicates an application or method optimized for the sequencing system.

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 8–10.5 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)

26–35B (single flow cell)c

52–70B (dual flow cells)c,e
Max read length 2 × 300 bp 2 × 250 bp 2 × 300 bp
Key applications and methodsf

Large whole-genome sequencing
(human, plant, animal)

  
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Small whole-genome sequencing
(microbe, virus)
checkmark
checkmark
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Exome and large panel sequencing
(enrichment-based)
checkmark
checkmark
checkmark

Targeted gene sequencing
(amplicon-based, gene panel)
checkmark
checkmark
checkmark

Single-cell profiling
(scRNA-Seq, scDNA-Seq, oligo tagging assays)
checkmark
checkmark
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Transcriptome sequencing
(total RNA-Seq, mRNA-Seq, gene expression profiling)
checkmark
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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)
checkmark
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Cell-free sequencing and liquid biopsy analysis
checkmark
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Explore NextSeq 1000 and 2000 Systems

Order

Explore NovaSeq 6000 System

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Explore NovaSeq X Series

Order
  1. Specifications are 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. 
  2. Specifications are based on a single flow cell run of S4 flow cell using Illumina PhiX control library at supported cluster densities.
  3. Specifications are 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.
  4. 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 System.
  5. Dual flow cell runs only apply to the NovaSeq X Plus System.
  6. 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 system 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 system categories with key factors to consider
  • Considerations around applications and data analysis
  • NGS buyer’s checklist

NGS Workflow Finder

Take the guesswork out of your next workflow. The NGS Workflow Finder provides personalized solution recommendations and resources so you can sequence with confidence.

Find your NGS workflow today

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Purchasing solutions

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Interested in a system demo or in speaking with someone?

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