Cost of Next-Generation Sequencing

Redefining the Price of Discovery

Redefining the Price of Discovery

Since the completion of the Human Genome Project, the cost of next-generation sequencing (NGS) has decreased at a dramatic rate, outpacing Moore’s Law. Through continuous innovation, Illumina has helped reduce the cost of NGS, enabling the $1000 human genome.

As next-generation sequencing costs continue to decline, Illumina is leading the way in making NGS more affordable and accessible. We strive to help labs of all sizes access the potential of this powerful technology. With these resources, we’ll guide you through key factors to consider when planning your NGS budget.

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Next-Generation Sequencing Cost Comparison

When evaluating NGS costs, consider the sample volume for your study. In general, for analyzing only a few (< 20) targets on a few samples, traditional methods such as Sanger sequencing or qPCR can be useful. For sequencing more than 20 target regions or high sample volumes, NGS is preferable.

NGS also delivers higher discovery power and sensitivity to detect novel or rare variants. It offers a hypothesis-free approach that doesn’t require prior knowledge of sequence information. These insights can be invaluable for enabling discovery and fueling research publications.

Learn more about:
NGS vs. qPCR
NGS vs. Sanger sequencing
NGS vs. microarrays

Next-Generation Sequencing Cost Considerations

When estimating the cost of NGS, consider these factors:

  • Instrument purchase
  • Cost per sample (eg, DNA isolation, library prep, and sequencing reagents)
  • Data analysis and storage
  • Optional instrument support plan
  • Optional training and preventive maintenance

Also consider additional lab equipment, such as:

  • Nucleic acid quantitation instrument
  • Nucleic acid quality analyzer
  • Thermocycler
  • Ultrasonicator (used in some library prep methods)
  • Centrifuge
  • Common lab supplies (eg, pipettors, 96-well plates, centrifuge tubes)
Buyer's Guide to NGS Systems

Find tips to help you estimate next-generation sequencing costs and choose the right instrument for your lab.

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NGS Cost Consultation

Have questions about how next-generation sequencing fits into your budget? Connect with an Illumina representative.

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NGS Cost Consultation

Examples of NGS Cost Per Sample

Application Estimated Cost Per Sample Experimental Parameters
Targeted gene expression profiling $23 USD

Cost per sample calculation is based on a run using:

  • MiniSeq System
  • 65 targets
  • 1000× coverage
  • 1 × 150 bp read length
  • TruSeq Targeted RNA Expression custom panel kit
  • MiniSeq Reagent High Output 75-cycle kit
16S metagenomic sequencing $18 USD

Cost per sample calculation is based on a run using:

  • MiSeq System
  • 96 samples
  • 2 × 300 bp read length
  • Nextera XT index primers
  • MiSeq Reagent v3 600-cycle kit
Low-Cost NGS Instrument

Designed for simplicity, the iSeq 100 Sequencing System makes next-generation sequencing easier and more affordable than ever. Discover more—without the cost.

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Low-Cost NGS Instrument

Cost of NGS Data Analysis

The cost of NGS data storage and analysis is one of the most common questions for beginners. Three factors will influence your data analysis budget:

  • Licensing a data analysis software platform
  • Storing data (often part of the licensing cost)
  • Running data analysis apps (also known as the compute cost)

The compute cost can vary depending on the amount of sequencing data you analyze. To help you calculate the cost of NGS data analysis for your study, we've estimated the volume of data generated for common methods.

Data Output for Common NGS Applications
Application Estimated Data Output
Human whole-genome sequencing (at 30× coverage) ~120 Gb
Human exome sequencing (at 100× coverage) ~8 Gb
Microbial whole-genome sequencing ~300 Mb
16S rRNA sequencing ~60 Mb

1 megabase (Mb) = 1,000,000 bases
1 gigabase (Gb) = 1,000,000,000 bases

The volume of data generated is related to the sequencing coverage level for your experiment.

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BaseSpace Sequence Hub
Free Trial for NGS Data Analysis

Try data analysis apps in BaseSpace Sequence Hub free for 30 days, without instrument purchase. You’ll also receive 250 complimentary iCredits to cover additional storage or compute costs.

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NGS Experimental Design

Learn about read length, sequencing coverage, and more—everything you need for your first sequencing run.

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NGS Experimental Design


When setting aside lab space for your sequencer, make sure the space is protected from excessive vibrations or temperature fluctuations. If your lab does not have pre-PCR and post-PCR areas, consider establishing two separate rooms, or separate lab benches, to avoid PCR contamination in your NGS experiments.
While training and installation services are an option, specialized lab staff are not required for instrument maintenance. The iSeq 100 System, our most affordable sequencer, is designed to make self-installation simple. Our instruments contain built-in quality controls and can guide you through running a system check. We also offer comprehensive service plans, and our scientists and engineers are available to provide additional support and answer questions.

Designed for the iSeq 100 System, this grant writing assistance document can help you justify funding in your grant applications.
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With multiplex sequencing, you can pool multiple libraries together and sequence them simultaneously. Multiplexing exponentially increases the number of samples analyzed in a single run, without drastically increasing cost or time.
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We have an equipment trade-in program, leasing options, and bundles to help you get started with NGS. Explore different buying options to find which best fits your needs.
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Use our interactive Sequencing Platform Comparison Tool to find the system that best suits your needs.
If you're interested in running BaseSpace or DRAGEN Cloud apps, you'll need a BaseSpace Sequence Hub subscription, plus iCredits for storing and analyzing your data. Learn more about iCredits and see the "Predicting Analysis Costs" table for guidance on estimating the cost of data analysis for various applications, including human whole-genome sequencing, exome sequencing, and 16S metagenomics.