Illumina NextSeq 550

NextSeq 550 is a sequencer released by Illumina in January 2014. It is based on Sequencing by Synthesis (SBS).

Illumina NextSeq 550
Photo of NextSeq 550: by Illumina

NextSeq 550 is available in the following models:
  • NextSeq 500 High-Output
  • NextSeq 500 Mid-Output
  • NextSeq 500 v2 High-Output
  • NextSeq 500 v2 Mid-Output


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date January 2014
Price [2] $275,000
MSRP as of March 2024
Type Benchtop
Weight 83 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina NextSeq 500 High-Output: 1x75bp to 2x150bp
Illumina NextSeq 500 Mid-Output: 2x75 to 2x150bp
Illumina NextSeq 500 v2 High-Output: 1x75bp to 2x150bp
Illumina NextSeq 500 v2 Mid-Output: 2x75 to 2x150bp
Run time Illumina NextSeq 500 High-Output: 11 to 29 hours
Illumina NextSeq 500 Mid-Output: 15 to 26 hours
Illumina NextSeq 500 v2 High-Output: 11 to 29 hours
Illumina NextSeq 500 v2 Mid-Output: 15 to 26 hours
Reagent cost per Gb [1] Illumina NextSeq 500 High-Output: $48.58
Illumina NextSeq 500 Mid-Output: $57.26
Illumina NextSeq 500 v2 High-Output: $48.58
Illumina NextSeq 500 v2 Mid-Output: $57.26
Data quality [3] Illumina NextSeq 500 High-Output: > 80% bases higher than Q30
Illumina NextSeq 500 Mid-Output: > 80% bases higher than Q30
Illumina NextSeq 500 v2 High-Output: > 80% bases higher than Q30
Illumina NextSeq 500 v2 Mid-Output: > 80% bases higher than Q30
Maximum output per run (Gb)[4] Illumina NextSeq 500 High-Output: 120.00
Illumina NextSeq 500 Mid-Output: 39.00
Illumina NextSeq 500 v2 High-Output: 120.00
Illumina NextSeq 500 v2 Mid-Output: 39.00
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 550

The NextSeq 550 sequencing system, launched by Illumina in 2014, falls into the category of benchtop next-generation sequencing (NGS) instruments targeting researchers with moderate throughput requirements. It is considered a successor to the earlier Illumina NextSeq 500, offering improvements in speed and scalability. While it has since been succeeded by the NextSeq 2000 with higher output capabilities, the NextSeq 550 remains a valuable option for labs seeking a cost-effective solution for targeted sequencing applications.

Key Innovations

  • Dual-configuration flow cell: The NextSeq 550 incorporates a dual-configuration flow cell, enabling researchers to choose between high-output and mid-output before each sequencing run dependent on their needs.
  • Two-channel chemistry: The NextSeq 550 leverages a two-channel chemistry system, reducing instrument complexity compared to four-channel systems used in higher-throughput sequencers. This streamlined approach translates to a more compact instrument footprint, minimizing laboratory space requirements. Additionally, the two-channel design enables very fast imaging, contributing to faster run times.

Features and Technologies

  • Load-and-go design: The system prioritizes user-friendliness with an intuitive interface and pre-filled reagent cartridges.
  • Scalable output: Researchers can tailor the run output, with configurations ranging from high-throughput (up to 120 Gb) to mid-output for more focused projects.
  • Illumina SBS Chemistry: The NextSeq 550 continues Illumina's tradition of accurate sequencing by synthesis (SBS) chemistry.
  • Data Quality: Base calling accuracy remains in line with other Illumina sequencers, exceeding 99%.

Intended Uses and Specific Applications

The NextSeq 550 caters to a wide range of targeted NGS applications, including:

  • Exome sequencing: Analyzing the protein-coding regions of the genome for variant discovery. Paired with kits like the Nextera Rapid Capture Exome Enrichment Kit.
  • Targeted panel sequencing: Focusing on specific regions of interest for mutation analysis in genes associated with diseases or traits. Compatible with various Illumina custom panel kits.
  • Transcriptome sequencing (RNA-seq): Identifying and quantifying RNA transcripts to understand gene expression. Works well with kits like the TruSeq Stranded mRNA Library Prep Kit.

These applications benefit from the instrument's ability to generate high-quality data for targeted regions with moderate throughput requirements.

Comparison with Competing Instruments

  • Illumina NextSeq 1000/2000: These sequencers offer significantly higher data output (up to 360 Gb) but come with a larger footprint, higher upfront cost, and increased reagent expenses. They are better suited for large-scale whole-genome sequencing projects.
  • PacBio Onso: This platform utilizes PacBio technology, enabling researchers to sequence with very high accuracy. It can also offer higher max output than the NextSeq 550 at a slightly lower upfront cost. However, Onso has longer run times.
  • Complete Genomics DNBSEQ-G99: This instrument offers sequencing at similar read lengths at much faster run times and higher accuracy, although the max output is smaller and it doesn’t have two different configurations, like the NextSeq 550.

Special Considerations

The NextSeq 550 is a compelling choice for researchers seeking a user-friendly, cost-effective benchtop sequencer for targeted NGS applications. Its strengths lie in its ease of use, scalability, and compatibility with established Illumina library prep workflows. However, labs with high-throughput whole-genome sequencing needs or those requiring long-read sequencing capabilities may find alternative platforms more suitable.

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This information on this page is up-to-date as of April 25, 2024 and based on the spec sheets published by the manufacturer.