NextSeq 550 System


The NextSeq 550 system is a single solution that provides a seamless transition between high-throughput sequencing and array scanning.

Supported BeadChips

CytoSNP-850K BeadChip—Uses the Infinium HD Super Assay

HumanCytoSNP-12 BeadChip—Uses the Infinium HD Ultra Assay

HumanKaryomap-12 BeadChip—Uses the Infinium Karyomapping Assay

Sequencing Consumables

NextSeq 500/550 High Output Kit—Available in three sizes (300 cycles, 150 cycles, and 75 cycles), the NextSeq 500/550 High Output Kit includes a high-output flow cell, a high-output reagent cartridge, and a buffer cartridge.

NextSeq 500/550 Mid Output Kit—Available in two sizes (300 cycles and 150 cycles), the NextSeq 500/550 Mid Output Kit includes a mid-output flow cell, a mid-output reagent cartridge, and a buffer cartridge.

Current Software

NextSeq Control Software—The control software interface guides you through the steps to load the flow cell and reagents for a sequencing run, or to load the BeadChip and adapter for scanning. During sequencing, the control software operates the imaging stage, dispenses reagents, controls flow cell temperatures, and captures images of clusters on the flow cell. During scanning, the control software operates the imaging stage and captures images of samples on the BeadChip.

Real-Time Analysis—The NextSeq system uses an updated implementation of Real-Time Analysis (RTA) called RTA v2, which includes important architecture differences from RTA used on other Illumina sequencing systems. Unlike earlier versions of RTA, all processes are performed in memory to maximize processing speed. RTA is part of the NextSeq system software.

Scanning Analysis Solutions

Array scanning data generated on the NextSeq 550 system can be analyzed with the BlueFuse Multi software. Data are generated in a compatible genotype type (GTC) file format.

Sequencing Analysis Solutions

The NextSeq system integrates with BaseSpace, providing an end to end data storage, sharing, and analysis system for sequencing output. The NextSeq system seamlessly streams data to BaseSpace, where demultiplexing and conversion to industry-standard FASTQ file formats occurs automatically.

Use bcl2fastq2 Conversion Software to convert NextSeq sequencing output to standard FASTQ file formats for downstream analysis using third-party analysis solutions. For more information, see bcl2fastq2 Conversion Software.

Illumina NextSeq 500