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.

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

Key NGS applications and methods^f
				New
Key specifications	iSeq 100 System	MiniSeq System	MiSeq System	MiSeq i100 Series^a	NextSeq 550 System	NextSeq 1000 and 2000 Systems
Max output per flow cell	1.2 Gb ^b	7.5 Gb ^c	15 Gb ^d	30 Gb ^a	120 Gb ^c	540 Gb ^e
Run time (range)^e	~9.5–19 hr	~5–24 hr	~5.5–56 hr	~4–15.5 hr	~11–29 hr	~8–44 hr
Max reads per run (single reads)	4M ^ab	25M ^c	25M ^d	100M ^a	400M ^c	1.8B ^e
Max read length	2 × 150 bp	2 × 150 bp	2 × 300 bp	2 × 300 bp	2 × 150 bp	2 × 300 bp
Small whole-genome sequencing (microbe, virus)	checkmark	checkmark	checkmark	checkmark	checkmark	checkmark
Exome and large panel sequencing (enrichment-based)					checkmark	checkmark
Targeted gene sequencing (amplicon-based, gene panel)	checkmark	checkmark	checkmark	checkmark	checkmark	checkmark
Single-cell profiling (scRNA-Seq, scDNA-Seq, oligo tagging assays)				checkmark	checkmark	checkmark
Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)				checkmark	checkmark	checkmark
Targeted gene expression profiling	checkmark	checkmark	checkmark	checkmark	checkmark	checkmark
miRNA and small RNA analysis	checkmark	checkmark	checkmark	checkmark	checkmark	checkmark
DNA–protein interaction analysis (ChIP-Seq)			checkmark	checkmark	checkmark	checkmark
Methylation sequencing				checkmark	checkmark	checkmark
16S metagenomic sequencing		checkmark	checkmark	checkmark	checkmark	checkmark
Metagenomic profiling (shotgun metagenomics, metatranscriptomics)				checkmark	checkmark	checkmark
Cell-free sequencing and liquid biopsy analysis				checkmark	checkmark	checkmark
	Explore iSeq 100 System Order	Explore MiniSeq System Order	Explore MiSeq System Order	Explore MiSeq i100 Series Order	Explore NextSeq 550 System Order	Explore NextSeq 1000 and 2000 Systems Order

Max range based on 100M flow cell specifications. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Specifications are based on the iSeq 100 i1 Reagents v2 (300 cycle) kit using Illumina PhiX control library at supported cluster densities.
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.
Specifications are based on a single flow cell run of the v3 flow cell using Illumina PhiX control library at supported cluster densities.
Run times includes cluster generation, sequencing, base calling, and quality scoring.
Checkmark indicates an application or method optimized for the sequencing system.

Production-scale sequencers

Key applications and methods^g
Key specifications	NextSeq 1000 and 2000 Systems	NovaSeq 6000 System	NovaSeq X Series
Max output per flow cell	540 Gb^a	3 Tb^b	8 Tb^c
Run time (range)^d	~8–44 hr	~13–44 hr	~17–48 hr
Max reads per run (single reads)	1.8B^a	10B (single flow cell)^b 20B (dual flow cells)^b	26B (single flow cell)^c 52B (dual flow cells)^c,f
Max read length	2 × 300 bp	2 × 250 bp	2 × 150 bp
Large whole-genome sequencing (human, plant, animal)		checkmark Icon not available	checkmark
Small whole-genome sequencing (microbe, virus)	checkmark	checkmark	checkmark
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	checkmark
Transcriptome sequencing (total RNA-Seq, mRNA-Seq, gene expression profiling)	checkmark	checkmark	checkmark
Chromatin analysis (ATAC-Seq, ChIP-Seq)	checkmark	checkmark	checkmark
Methylation sequencing	checkmark	checkmark	checkmark
Metagenomic profiling (shotgun metagenomics, metatranscriptomics)	checkmark	checkmark	checkmark
Cell-free sequencing and liquid biopsy analysis	checkmark	checkmark	checkmark
	Explore NextSeq 1000 and 2000 Systems Order	Explore NovaSeq 6000 System Order	Explore NovaSeq X Series Order

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.
Specifications are based on a single flow cell run of S4 flow cell using Illumina PhiX control library at supported cluster densities.
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.
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.
Max range based on 100M flow cell specifications. 50M and 100M flow cells will be available starting in 2025 for the MiSeq i100 Plus System only.
Dual flow cell runs only apply to the NovaSeq X Plus System.
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.

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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?

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

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.

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For every lab, everywhere

NextSeq 1000 and NextSeq 2000 Reagents

Sequencing platform comparison

DRAGEN v4.3 now available on-premises and on-cloud

Illumina Proactive Instrument Performance Service

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Next-generation sequencing for beginners

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This is the Genome Era

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Illumina DRAGEN secondary analysis v4.3

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For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

For every lab, everywhere

Sequencing platforms

Benchtop sequencers

Production-scale sequencers

NGS platforms for a growing sequencing community

How to choose an NGS platform

Methods

Software needs

Technology and support

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

NGS Workflow Finder

Related links

Purchasing solutions

Interested in a system demo or in speaking with someone?