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Illumina NextSeq 550

The Illumina NextSeq® 550 is the largest desktop next-generation sequencing (NGS) system from Illumina capable of sequencing a 30x human genome in a single run. Two different flow cell options and multiple reagent configurations are providing a maximum application flexibility (130 to 400M clusters; 40 to 120 Gb).

Accordingly, the system is suitable for a high number of different applications, e.g. whole exome- or genome sequencing, RNAseq, targeted resequencing or gene expression profiling and single-cell sequencing. The sequencing technology is based surface-based bridge amplification for clonal amplification and sequencing of each generated cluster using the Illumina "sequencing by synthesis" (SBS) method with reversible terminator chemistry.


  • Scalability (20–120 Gb) in a single run supporting a broad range of applications and study sizes
  • Sequencing runs, including on-board cluster generation, complete in 12–30 hours
  • Proven SBS chemistry with single-base extension enables accurate sequencing of homopolymers (sometimes a problem on the IonTorrent system)
  • Fully automated paired-end sequencing
  • Automated BeadChip array scanning and image file generation
  • Approximately 7000 peer-reviewed publications have been published using Illumina SBS sequence data, and more than 24,000 peer-reviewed publications have been published using Illumina array technology
  • Number of reads per run
  • preadjustment of library diversity is required for optimum sequence quality

Data Generation

Throughput per run

  • Up to 400 million reads per run (eg, clusters passing filter) using High Output flow cell
  • Up to 130 million reads per run (eg, clusters passing filter) using Mid Output flow cell

Sequencing flexibility

  • 100–120 Gb data per 2 × 150 bp run using High Output flow cell and reagents
  • 33–40 Gb data per 2 × 150 bp run using Mid Output flow cell and reagents
  • Set-up options include single-read or paired-end runs

Array Scanning

  • Flow cell options (eg, Mid or High Output flow cells) can be used to select data output levels
  • Read length is fully adjustable up to 300 base pairs
  • Single array imaged per scanning session
  • Up to 12 samples imaged per run with current array support



  • 12 light-emitting diodes at 520 nm, 650 nm

Instrument Control Computer

  • Dual Intel Xeon E5-2448L 1.8 GHz CPU with 96 GB of RAM included for instrument control, processing images, and base calling
  • Conducts real-time analysis processing that automatically produces image intensities and quality-scored base calls directly on the instrument computer

Sequencing run time

  • ~ 12 hours for a 1 × 75 bp single-read sequencing run
  • ~ 18 hours for a 2 × 75 bp paired-read sequencing run
  • ~ 30 hours for a 2 × 150 bp paired-read sequencing run