Sequencing Platform Comparison Tool

This tool will help you compare next-generation sequencing systems and find the one that's right for your lab or application

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†
Output Range > 5 Gb
Run Time 24 hours
Reads per Run > 15 million
Maximum Read Length in Dx Mode 2 × 150 bp
Samples per Run 8-96 samples/run depending on assay
Relative Price per Sample Mid Cost
Relative Instrument Price Low Cost
Learn More System Summary
Downloads Spec Sheet
System Overview MiSeqDx Overview
 
NextSeq 550Dx†
Output Range ≥ 90 Gb
Run Time < 35 hours
Reads per Run > 300 million
Maximum Read Length 2 × 150 bp
Samples per Run 8-96 samples/run depending on assay
Relative Price per Sample Mid Cost
Relative Instrument Price Mid Cost
Learn More System Summary
Downloads Spec Sheet
System Overview NextSeq 550Dx Overview
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 regulated MiSeqDx system.

At the heart of the system is the FDA regulated 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 TruSeq Custom Amplicon Kit Dx 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
MiSeqDx Overview
NextSeq 550Dx†

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 NextSeq 550Dx system.

The NextSeq 550Dx Instrument is FDA regulated and CE-IVD marked, enabling clinical laboratories to develop and perform a wide range of applications, from NGS IVD assays using targeted panels, to clinical research applications that include methods from targeted panels to exomes. Paired with the TruSeq Custom Amplicon Kit Dx and the NextSeq 550Dx High Output Reagent Kit, the NextSeq 550Dx is part of an IVD development toolkit that enables clinical labs to design clinical assays with regulated components.*

NextSeq 550Dx Overview
Contact Me Molecular Diagnostics
  • Contact your Illumina representative for more information about IVD development partnerships.
  • For In Vitro Diagnostic Use (except as specifically noted).
 
MiSeqFGx
Output Range 0.3-15 Gb
Run Time 4-55 hours
Reads per Run 1-25 million
Maximum Read Length 2 × 300 bp
Samples per Run N/A
Relative Price per Sample Mid Cost
Relative Instrument Price Mid Cost
Learn More System Summary
Downloads Spec Sheet
System Overview MiSeqDx Overview

MiSeq FGx System

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
MiSeqFGx Overview
Contact Me Forensic Genomics
  No longer available
HiSeq X Five†
Output Range 900-1800 Gb
Run Time < 3 days
Reads per Run 3-6 billion
Maximum Read Length 2 × 150 bp
Samples per Run§ 8-16
Relative Price per Sample§ Higher Cost
Relative Instrument Price§ Lower Cost
Downloads Spec Sheet
System Overview HiSeq Series Overview
  No longer available
HiSeq X Ten†
Output Range 900-1800 Gb
Run Time < 3 days
Reads per Run 3-6 billion
Maximum Read Length 2 × 150 bp
Samples per Run§ 8-16
Relative Price per Sample§ Lower Cost
Relative Instrument Price§ Higher Cost
Downloads Spec Sheet
System Overview HiSeq Series Overview
 
NovaSeq 6000
Output Range 134-6000 Gb‡
Run Time 24-44 hr
Reads per Run Up to 20 billion‡
Maximum Read Length 2 × 150 bp
Samples per Run§ 4-48
Relative Price per Sample§ Higher Cost
Relative Instrument Price§ Lower Cost
Downloads Spec Sheet
System Overview NovaSeq Overview
Contact Me
  • 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.
  • Lower limits of output and reads per run ranges based on a single S1 flow cell run; upper limits based on dual S4 flow cell run. Run times include cluster generation, sequencing, and base calling. Run times are based on running two flow cells of the same type. Starting two different flow cells will impact run time. NovaSeq S1 Reagent Kits are not currently available.
  • 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.
 
iSeq 100*
Output Range 1.2 Gb
Run Time 9–19 hr
Run Time 7–17.5 hr
Reads per Run 4 million
Maximum Read Length 2 × 150 bp
Samples per Run§ 1–8
Samples per Run‡ 1–8
Samples per Run§ 1–48
Samples per Run‡ 1–8
Samples per Run‡ 1–2
Samples per Run‡ 1–8
Relative Price per Sample‡ Highest Cost
Relative Instrument Price‡ Lowest Cost
Downloads Spec Sheet
System Overview iSeq Overview
 
MiniSeq
Output Range 1.8–7.5 Gb
Run Time 4–24 hr
Run Time 24 hr
Reads per Run 8–25 million
Maximum Read Length 2 × 150 bp
Samples per Run‡ N/A
Samples per Run§ 50
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 × 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
 
NextSeq*†
Output Range 20–120 Gb
Run Time 11–29 hr
Reads per Run 130–400 million
Maximum Read Length 2 × 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‡ Highest Cost
Relative Instrument Price‡ Lowest Cost
Downloads Spec Sheet
System Overview NextSeq Overview
  No longer available
HiSeq 4000*
Output Range 125–1500 Gb
Run Time < 1–3.5 days
Reads per Run 2.5–5 billion
Maximum Read Length 2 × 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‡ High Cost
Downloads Spec Sheet
System Overview HiSeq Overview
 
NovaSeq 6000*††
Output Range 134–6000 Gb
Run Time 19–40 hr
Run Time 13–44 hr
Run Time 13–44 hr
Run Time 13–44 hr
Run Time 13–44 hr
Run Time 24–44 hr
Reads per Run Up to 20 billion
Maximum Read Length 2 × 150 bp
Samples per Run‡ 4–48
Samples per Run§ N/A
Samples per Run‡ 26–750
Samples per Run§ N/A
Samples per Run§ N/A
Samples per Run‡ 26–400
Samples per Run§ N/A
Samples per Run‡ 86–768
Samples per Run‡ 2–30
Samples per Run§ N/A
Relative Price per Sample‡ Lowest Cost
Relative Instrument Price‡ Higher Cost
Downloads Spec Sheet
System Overview NovaSeq Overview
Contact Me Cancer Genomics
  • For Research Use Only. Not for use in diagnostic procedures.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Large Whole-Genome Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Small Whole-Genome Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Exome Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Targeted RNA Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Whole-Transcriptome Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Small RNA Analysis in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform ChIP-Seq in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform Methylation Sequencing in Research Mode only.
  • In vitro diagnostic (IVD) instrument available. IVD instrument can perform 16S Metagenomic Sequencing in Research Mode only.
  • Samples per run assume capability to address individual lanes of the NovaSeq flow cell. They are based on 30X coverage of whole human genome at ≥ 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.
  • Samples per run assume capability to address individual lanes of the NovaSeq flow cell. Assumes ~8Gb per sample; 200 cycle kit for S1 & S2 and 300 cycle kit for S4. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
  • 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.
  • Samples per run assume capability to address individual lanes of the NovaSeq flow cell. Based on ≥ 50M reads at 2×50 bp. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
  • 5 million reads per sample. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
  • Samples per run assume capability to address individual lanes of the NovaSeq flow cell. Based on ≥ 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.
  • Samples per run assume capability to address individual lanes of the NovaSeq flow cell. Based on 200 Gb per sample at 30X coverage. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results. Based on 2×75 reads or greater.
  • Based on Nextera XT indexing. "Price per Sample" and "Instrument Price" relative to the other instruments shown in comparison results.
  • Lower limits of output and reads per run ranges based on a single S1 flow cell run; upper limits based on dual S4 flow cell run. Run times include cluster generation, sequencing, and base calling. Run times are based on running two flow cells of the same type. Starting two different flow cells will impact run time. NovaSeq S1 Reagent Kits are not currently available.
  • ** Maximum specs available with the NextSeq 2000 P3 Reagents, available late 2020; specifications subject to change