Sequencing Platform Comparison Tool

MiSeqDx

Next-generation sequencing (NGS) technology can provide a broad view of the human genome, helping us discover and apply relevant genomic information to human health. Ultimately, this may lead to more accurate diagnosis, prognosis, and therapeutic selection. Clinical laboratories can take advantage of the benefits of NGS with the FDA-cleared MiSeqDx system.

At the heart of the system is the FDA-cleared MiSeqDx instrument, stringently validated for design and performance. Two IVD assays and one IVD kit are currently available for use on the MiSeqDx instrument:

The MiSeqDx Universal Kit allows users to develop their own NGS laboratory tests, expanding their lab offerings to meet ever-evolving needs
The MiSeqDx Cystic Fibrosis 139-Variant Assay detects 139 clinically relevant and functionally verified CFTR variants
The MiSeqDx Cystic Fibrosis Clinical Sequencing Assay detects mutations within the protein coding regions and intron/exon boundaries of CFTR

MiSeq FGx

The MiSeq FGx Forensic Genomics System is the first fully validated sequencing system designed for use in forensic genomics applications. The complete sample-to-answer system uses dedicated library preparation kits, customized instrument control software, and an analytical software package to support the reliable analysis of both routine and challenging forensic samples.

The MiSeq FGx System workflow is easy-to-use, automated, and fast:

Compact, all-in-one platform incorporates cluster generation, paired-end fluidics, and SBS chemistry
Intuitive touch screen interface makes for simple instrument operation
Plug-and-play reagents with RFID tracking make for added speed and convenience


NovaSeq Series Scalable throughput and flexibility for a broad range of applications.	HiSeq X Ten & HiSeq X Five Ultra-high-throughput for whole-genome sequencing.

	NovaSeq System	HiSeq X Series*
	NovaSeq 6000^†	HiSeq X Five^†	HiSeq X Ten^†
Output Range	167–6000 Gb^‡	900–1800 Gb	900–1800 Gb
Run Time	19–40 hr	<3 days	<3 days
Reads per Run	1.4–20 billion^§	3–6 billion	3–6 billion
Maximum Read Length	2 × 150 bp	2 × 150 bp	2 × 150 bp
Samples per Run^\|	4–48	8–16	8–16
Relative Price per Sample^\|	Higher Cost	Higher Cost	Lower Cost
Relative Instrument Price^\|	Lower Cost	Lower Cost	Higher Cost
Downloads	Spec Sheet	Spec Sheet	Spec Sheet

* Specifications shown for an individual HiSeq X Sequencing System. HiSeq X is only available as part of the HiSeq X Five or HiSeq X Ten.

† For Research Use Only. Not for use in diagnostic procedures.

‡ Output Range is based on a dual flow cell run of S4 Flow Cells which have not been released; therefore, performance metrics are subject to change.

§ Reads Per Run is based on a dual flow cell run of S4 Flow Cells which have not been released; therefore, performance metrics are subject to change.

| Based on 30X coverage of a human genome, assumes minimum of 100Gb per genome. Sample number will vary for other species based on relative genome size.

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MiniSeq System Low-throughput targeted DNA and RNA sequencing.	MiSeq Series Small genome, amplicon, and targeted gene panel sequencing.	NextSeq System Exome, transcriptome, and targeted resequencing.	HiSeq System Production-scale genome, exome, transcriptome sequencing, and more.	NovaSeq Series Scalable throughput and flexibility for a broad range of applications.

	MiniSeq System	MiSeq Series			NextSeq System	HiSeq System	NovaSeq Series^††
	MiniSeq	MiSeq^*	MiSeqDx^†	MiSeq FGx^‡	NextSeq 500^*	HiSeq 4000^*	NovaSeq 5000^*	NovaSeq 6000^*
Output Range	1.8–7.5 Gb	0.3–15 Gb	0.3–15 Gb	0.3–15 Gb	20–120 Gb	125–1500 Gb	167—2000 Gb	167—6000 Gb
Run Time	4–24 hr	5–55 hr	4–55 hr	4–55 hr	11–29 hr	<1–3.5 days	TBA	19—40 hr
Reads per Run	8–25 million	1–25 million	1–25 million	1–25 million (for research)	130–400 million	2.5–5 billion	1.4–6.6 billion	1.4–20 billion
Max Read Length	2 × 150 bp	2 × 300 bp	2 × 300 bp	2 × 300 bp	2 × 150 bp	2 × 150 bp	2 × 150 bp	2 × 150 bp
Samples per Run^§	N/A	N/A	N/A	N/A	1	6–12	4—16	4—48
Samples per Run^§	1–384	1–384	N/A	1–96	96	768–1536	N/A	N/A
Samples per Run^§	N/A	N/A	N/A	N/A	8	50—100	32—132	32—192
Samples per Run^§	1–96	1–96	N/A	N/A	12–36	N/A	N/A	N/A
Samples per Run^§	1–384	1–384	N/A	N/A	1–384	1–6144	N/A	N/A
Samples per Run^§	N/A	N/A	N/A	N/A	2–8	50–100	32—132	32—192
Samples per Run^§	1–5	1–5	N/A	N/A	25–80	60–792	N/A	N/A
Samples per Run^§	1–6	1–6	N/A	N/A	8–24	160–320	96—192	96—192
Samples per Run^§	N/A	N/A	N/A	N/A	1	3–6	2—8	2–24
Samples per Run^§	1–384	1–384	N/A	N/A	1–384	N/A	N/A	N/A
Relative Price per Sample^§	Higher Cost	Higher Cost	Higher Cost	Higher Cost	Mid Cost	Lower Cost	Lower Cost	Lower Cost
Relative Instrument Price^§	Lower Cost	Lower Cost	Lower Cost	Lower Cost	Mid Cost	Higher Cost	Higher Cost	Higher Cost
Downloads	Spec Sheet	Spec Sheet	Spec Sheet	Spec Sheet	Spec Sheet	Spec Sheet	Spec Sheet	Spec Sheet

†† All output and read number specifications based on dual flow cell runs. Run time includes cluster generation, sequencing, and base calling for a Dual S2 Flow Cell Run on the NovaSeq 6000 System. Run times on the NovaSeq 5000 System may be slightly longer.

* For Research Use Only. Not for use in diagnostic procedures.

† For In Vitro Diagnostic applications.

‡ For Research, Forensic, and Paternity Use Only.

§ Based on 30X coverage of a human genome, assumes minimum of 100Gb per genome. Sample number will vary for other species based on relative genome size.

§ Based on 30X or greater coverage of a 5Mb microbial genome. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

§ Based on 8 Gb per sample at 2x75 bp. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 50M reads at 2x75bp or greater.

§ Based on TruSight One Sequencing Panel. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

§ 10 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

§ 50 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 50M reads at 2x50bp or greater.

§ 5 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

§ 15 million reads per sample for identification of transcription factor binding. Additional reads required for histone marks. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 15M reads at 1x50bp or greater.

§ 30X coverage. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 2x75 reads or greater.

§ Based on Nextera XT indexing. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

Let's begin with some information about the nature of your work.

What is your project type?

Research Use Only

Molecular Diagnostics

Forensic Genomics

What is your primary area of interest?

Cancer Genomics

Agrigenomics

Genetic Disease

Microbial Genomics

Reproductive Health

Population-scale WGS

Other Research Areas

What technique will you be using?

Large Whole-Genome Sequencing (human, plant, animal)

Small Whole-Genome Sequencing (microbe, virus)

Exome Sequencing

Targeted Gene Sequencing (amplicon, gene panel)

Targeted RNA Sequencing

Whole-Transcriptome Sequencing

Small RNA Analysis

ChIP-Seq

Methylation Sequencing

16S Metagenomic Sequencing

MiSeqDx System

At the heart of the system is the FDA-cleared MiSeqDx instrument, stringently validated for design and performance. Two IVD assays and one IVD kit are currently available for use on the MiSeqDx instrument:

The MiSeqDx Universal Kit allows users to develop their own NGS laboratory tests, expanding their lab offerings to meet ever-evolving needs
The MiSeqDx Cystic Fibrosis 139-Variant Assay detects 139 clinically relevant and functionally verified CFTR variants
The MiSeqDx Cystic Fibrosis Clinical Sequencing Assay detects mutations within the protein coding regions and intron/exon boundaries of CFTR

Contact Me Email Comparison Molecular Diagnostics

MiSeq FGx System

The MiSeq FGx System workflow is easy-to-use, automated, and fast:

Compact, all-in-one platform incorporates cluster generation, paired-end fluidics, and SBS chemistry
Intuitive touch screen interface makes for simple instrument operation
Plug-and-play reagents with RFID tracking make for added speed and convenience

Contact Me Email Comparison Forensic Genomics

	NovaSeq 6000
Output Range	167-6000 Gb
Run Time	19-40 hr
Reads per Run	1.4-20 billion^§
Maximum Read Length	2 x 150 bp
Samples per Run^Ι	4-48
Relative Price per Sample^Ι	Higher Cost
Relative Instrument Price^Ι	Lower Cost
Downloads	Spec Sheet
System Overview	NovaSeq Overview

	HiSeq X Five^†
Output Range	900-1800 Gb
Run Time	< 3 days
Reads per Run	3-6 billion
Maximum Read Length	2 x 150 bp
Samples per Run^Ι	8-16
Relative Price per Sample^Ι	Higher Cost
Relative Instrument Price^Ι	Lower Cost
Downloads	Spec Sheet
System Overview	HiSeq Series Overview

	HiSeq X Ten^†
Output Range	900-1800 Gb
Run Time	< 3 days
Reads per Run	3-6 billion
Maximum Read Length	2 x 150 bp
Samples per Run^Ι	8-16
Relative Price per Sample^Ι	Lower Cost
Relative Instrument Price^Ι	Higher Cost
Downloads	Spec Sheet
System Overview	HiSeq Series Overview

Specifications shown for an individual HiSeq X Sequencing System. HiSeq X is only available as part of the HiSeq X Five or HiSeq X Ten.
For Research Use Only. Not for use in diagnostic procedures.
Output Range is based on a dual flow cell run of S4 Flow Cells which have not been released; therefore, performance metrics are subject to change.
Reads Per Run is based on a dual flow cell run of S4 Flow Cells which have not been released; therefore, performance metrics are subject to change.
Based on 30X coverage of a human genome, assumes minimum of 100Gb per genome. Sample number will vary for other species based on relative genome size.

	MiniSeq
Output Range	1.8-7.5 Gb
Run Time	4-24 hr
Reads per Run	8-25 million
Maximum Read Length	2 x 150 bp
Samples per Run^§	N/A
Samples per Run^§	1-384
Samples per Run^§	N/A
Samples per Run^§	1-96
Samples per Run^§	1-384
Samples per Run^§	N/A
Samples per Run^§	1-5
Samples per Run^§	1-6
Samples per Run^§	N/A
Samples per Run^§	1-384
Relative Price per Sample^§	Higher Cost
Relative Instrument Price^§	Lower Cost
Downloads	Spec Sheet
System Overview	MiniSeq Overview

	MiSeq^*
Output Range	0.3-15 Gb
Run Time	5-55 hr
Reads per Run	1-25 million
Maximum Read Length	2 x 300 bp
Samples per Run^§	N/A
Samples per Run^§	1-384
Samples per Run^§	N/A
Samples per Run^§	1-96
Samples per Run^§	1-384
Samples per Run^§	N/A
Samples per Run^§	1-5
Samples per Run^§	1-6
Samples per Run^§	N/A
Samples per Run^§	1-384
Relative Price per Sample^§	Mid Cost
Relative Instrument Price^§	Mid Cost
Downloads	Spec Sheet
System Overview	MiSeq Overview

	MiSeq Dx^†
Output Range	0.3-15 Gb
Run Time	4-55 hr
Reads per Run	1-25 million
Maximum Read Length	2 x 300 bp
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Relative Price per Sample^§	Mid Cost
Relative Instrument Price^§	Mid Cost
Downloads	Spec Sheet
System Overview	MiSeq Dx Overview

	MiSeq FGx^‡
Output Range	0.3-15 Gb
Run Time	4-55 hr
Reads per Run	1-25 million (for research)
Maximum Read Length	2 x 300 bp
Samples per Run^§	N/A
Samples per Run^§	1-96
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	N/A
Relative Price per Sample^§	Mid Cost
Relative Instrument Price^§	Mid Cost
Downloads	Spec Sheet
System Overview	MiSeq FGx Overview

	NextSeq^*
Output Range	20-120 Gb
Run Time	11-29 hr
Reads per Run	130-400 million
Maximum Read Length	2 x 150 bp
Samples per Run^§	1
Samples per Run^§	96
Samples per Run^§	8
Samples per Run^§	12-36
Samples per Run^§	1-384
Samples per Run^§	2-8
Samples per Run^§	25-80
Samples per Run^§	8-24
Samples per Run^§	1
Samples per Run^§	1-384
Relative Price per Sample^§	Lower Cost
Relative Instrument Price^§	Higher Cost
Downloads	Spec Sheet
System Overview	NextSeq Overview

	HiSeq 4000^*
Output Range	125-1500 Gb
Run Time	<1-3.5 days
Reads per Run	2.5-5 billion
Maximum Read Length	2 x 150 bp
Samples per Run^§	6-12
Samples per Run^§	768-1536
Samples per Run^§	50-100
Samples per Run^§	N/A
Samples per Run^§	1-6144
Samples per Run^§	50-100
Samples per Run^§	60-792
Samples per Run^§	160-320
Samples per Run^§	3-6
Samples per Run^§	N/A
Relative Price per Sample^§	Lower Cost
Relative Instrument Price^§	Higher Cost
Downloads	Spec Sheet
System Overview	HiSeq Overview

	NovaSeq 5000^††*
Output Range	167-2000 Gb
Run Time	TBA
Reads per Run	1.4-6.6 billion
Maximum Read Length	2 x 150 bp
Samples per Run^§	4-16
Samples per Run^§	N/A
Samples per Run^§	32-132
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	32-132
Samples per Run^§	N/A
Samples per Run^§	96-192
Samples per Run^§	2-8
Samples per Run^§	N/A
Relative Price per Sample^§	Lower Cost
Relative Instrument Price^§	Higher Cost
Downloads	Spec Sheet
System Overview	NovaSeq Overview

	NovaSeq 6000^††*
Output Range	167-6000 Gb
Run Time	19-40 hr
Reads per Run	1.4-20 billion
Maximum Read Length	2 x 150 bp
Samples per Run^§	4-48
Samples per Run^§	N/A
Samples per Run^§	32-192
Samples per Run^§	N/A
Samples per Run^§	N/A
Samples per Run^§	32-192
Samples per Run^§	N/A
Samples per Run^§	96-192
Samples per Run^§	2-24
Samples per Run^§	N/A
Relative Price per Sample^§	Lower Cost
Relative Instrument Price^§	Higher Cost
Downloads	Spec Sheet
System Overview	NovaSeq Overview

All output and read number specifications based on dual flow cell runs. Run time includes cluster generation, sequencing, and base calling for a Dual S2 Flow Cell Run on the NovaSeq 6000 System. Run times on the NovaSeq 5000 System may be slightly longer.
For Research Use Only. Not for use in diagnostic procedures.
For In Vitro Diagnostic applications.
For Research, Forensic, and Paternity Use Only.
Based on 30X coverage of a human genome, assumes minimum of 100Gb per genome. Sample number will vary for other species based on relative genome size.
Based on 30X or greater coverage of a 5Mb microbial genome. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
Based on 8 Gb per sample at 2x75 bp. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 50M reads at 2x75bp or greater.
Based on TruSight One Sequencing Panel. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
10 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
50 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 50M reads at 2x50bp or greater.
5 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
15 million reads per sample for identification of transcription factor binding. Additional reads required for histone marks. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 15M reads at 1x50bp or greater.
30X coverage. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 2x75 reads or greater.
Based on Nextera XT indexing. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.

MiSeqDx

MiSeq FGx

NovaSeq Series

HiSeq X Ten & HiSeq X Five

[application here]

MiniSeq System

MiSeq Series

NextSeq System

HiSeq System

NovaSeq Series