Illumina NextSeq 1000/2000

NextSeq 1000/2000 is a sequencer released by Illumina in October 2020. It is based on Sequencing by Synthesis (SBS).

Illumina NextSeq 1000/2000
Image of NextSeq 2000: by Illumina

NextSeq 1000/2000 is available in the following models:
  • NextSeq 1000/2000 P1
  • NextSeq 1000/2000 P2
  • NextSeq 1000/2000 P3


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date October 2020
Price [2] $335,000
The NextSeq 1000 has a list price of $210,000 and the NextSeq 2000 has a list price of $335,000 MSRP as of March 2024
Type Benchtop
Weight 141 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina NextSeq 1000/2000 P1: 1x300bp, 2x150bp
Illumina NextSeq 1000/2000 P2: 1x300bp, 2x150bp
Illumina NextSeq 1000/2000 P3: 1x300bp, 2x150bp
Run time Illumina NextSeq 1000/2000 P1: 10 to 34 hours
Illumina NextSeq 1000/2000 P2: 13 to 44 hours
Illumina NextSeq 1000/2000 P3: 11 to 48 hours
Reagent cost per Gb [1] Illumina NextSeq 1000/2000 P1: $31.67
Illumina NextSeq 1000/2000 P2: $21.94
Illumina NextSeq 1000/2000 P3: $17.08
Data quality [3] Illumina NextSeq 1000/2000 P1: ≥ 90% of bases higher than Q30
Illumina NextSeq 1000/2000 P2: ≥ 90% of bases higher than Q30
Illumina NextSeq 1000/2000 P3: ≥ 90% of bases higher than Q30
Maximum output per run (Gb)[4] Illumina NextSeq 1000/2000 P1: 60.00
Illumina NextSeq 1000/2000 P2: 180.00
Illumina NextSeq 1000/2000 P3: 360.00
Primary error type [5] Substitutions
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the NextSeq 1000/2000

Illumina's NextSeq 1000 and NextSeq 2000 sequencing systems are versatile and powerful instruments designed for life science researchers who need flexible tools for a variety of sequencing applications. The NextSeq series bridges the gap between Illumina's smaller benchtop sequencers (iSeq, MiniSeq) and the high-throughput production-scale NovaSeq systems. The NextSeq 1000/2000 platforms are successors to the popular NextSeq 500/550, offering significant improvements in throughput, cost efficiency, and ease of use.

Key Innovations

The NextSeq 1000/2000 leverage several key innovations that enable increased throughput and flexibility:

  • Patterned Flow Cells: These flow cells represent a significant advancement in sequencing technology. They incorporate a nanowell structure etched onto the glass surface. These nanowells confine individually amplified DNA molecules (clusters) to designated locations on the flow cell. The tighter confinement of clusters compared to earlier flow cell designs increases the packing density of clusters on the flow cell. This increased density allows for a higher number of clusters to be sequenced in a single run, ultimately resulting in significantly more data output.
  • Super Resolution Optics System: This new optical system is designed specifically to handle the higher cluster densities achieved with patterned flow cells. Traditional sequencing optics rely on diffraction-limited resolution, which can struggle to distinguish between closely spaced clusters. The Super Resolution Optics System utilizes advanced lens designs and illumination techniques to overcome these limitations. By incorporating specialized filters and precise focusing mechanisms, this system reduces the halo effect (crosstalk between neighboring clusters) and improves the signal-to-noise ratio. This translates to clearer and more accurate detection of fluorescent signals from smaller and denser clusters, ultimately enhancing data quality and base calling accuracy.
  • Two-Channel SBS Chemistry: Traditional SBS sequencing relies on four fluorescent dyes (one for each DNA base: A, C, G, and T) to identify the incorporated base during each sequencing cycle. However, as cluster densities increase on patterned flow cells, the physical separation between these dyes can become too small for optimal signal distinction. The NextSeq 1000/2000 address this challenge by employing a novel two-channel SBS chemistry approach. In this system, only two fluorescent dye, blue and green, are used per cycle, with each dye combination—both, neither, single green, and single blue—are capable of differentiating between all 4 bases. This two-channel approach reduces the overall number of dyes needed within the nanowell, minimizing crosstalk and enabling clear and accurate base calling for the high-density clusters on patterned flow cells.

Features and Technologies

  • Scalable Throughput: The NextSeq 1000/2000 offer a range of flow cell options (P1, P2, P3), allowing users to match output requirements to their project's needs. The P3 flow cell, exclusive to the NextSeq 2000, can generate up to 1.2 billion reads.
  • Integrated DRAGEN Analysis System: The NextSeq 1000/2000 come equipped with Illumina's DRAGEN Secondary Analysis system, a powerful suite of secondary analysis tools embedded directly on the instrument. This integration streamlines the data analysis workflow by eliminating the need for transferring large sequencing datasets to separate computing clusters. DRAGEN enables researchers to perform on-instrument analysis of sequencing data directly following a run. Examples of supported pipelines are alignment, variant calling, and RNA-Seq analysis. This onboard analysis capability significantly reduces turnaround time for data analysis, allowing researchers to interpret their results faster and accelerate their scientific discoveries.
  • Simplified Workflow: The cartridge-based reagent system and intuitive touch screen interface make the NextSeq 1000/2000 straightforward to operate.
  • Data Quality: Illumina's proven Sequencing By Synthesis (SBS) chemistry maintains high accuracy standards, with average Q30 scores exceeding 90% for all flow cells for the shorter read lengths.

Intended Uses and Specific Applications

The NextSeq 1000/2000 are well-suited for various sequencing applications:

  • Whole Genome Sequencing (WGS): Ideal for human WGS (up to 30x coverage) as well as microbial or targeted genome sequencing. Compatible with Illumina's TruSeq DNA PCR-Free Kit.
  • RNA Sequencing (RNA-Seq): Investigate gene expression, differential expression, and transcript discovery. Compatible with Illumina's Stranded mRNA and Stranded Total RNA prep kits.
  • Exome Sequencing: Focus on protein-coding regions of the genome. Compatible with Illumina's TruSeq Exome Kit and IDT xGen Exome Research Panel.
  • Other Applications: Targeted panels, metagenomics, single-cell sequencing, and more.

Comparison with Competing Instruments

  • Illumina NextSeq 550 The NextSeq 1000/2000 significantly outperform their predecessors in output, cost-effectiveness, and user-friendliness, although the upfront cost is higher
  • Singular Genomics G4: The G4 offers comparable throughput and is faster on average, especially for higher output. However, the NextSeq 1000/2000 has a slightly better upfront cost and is more accurate, especially for shorter read lengths.
  • Element Biosciences AVITI: The AVITI system boasts a lower upfront cost and reagent costs. However, the NextSeq 1000/2000 may hold an advantage in established workflows and data quality metrics due to Illumina's widespread use.

Special Considerations

The NextSeq 1000/2000 are excellent choices when:

  • Flexibility is paramount: The range of flow cell configurations caters to diverse project needs.
  • Accuracy and reliability are essential: Illumina's SBS chemistry offers proven performance.
  • Workflow efficiency matters: Simplified setup, integrated analysis options, and accessible operation make it a user-friendly system.

Need sequencing done on a Illumina NextSeq 1000/2000 or a specific instrument? Tell us about your project here, and we'll connect you with a qualified provider.

This information on this page is up-to-date as of April 12, 2024 and based on the spec sheets published by the manufacturer.