NextSeq 550 System applications and methods

A wide world of inquiry

Harness next-generation sequencing and array technologies to do more with a single system 

NextSeq 550 flow cell

Key applications and methods

The NextSeq 550 System RNA sequencing solution enables researchers to examine gene expression and identify isoforms, novel transcripts, and gene fusions. mRNA sequencing delivers a detailed snapshot of the coding transcriptome, enabling sequencing of up to 16 transcriptomes per run.

See how researchers use mRNA-Seq with the NextSeq 550 System:

Sifting through cells

Discovering cancer biomarkers

NextSeq 550 System RNA-Seq application note


The NextSeq 550 System offers a simple and reliable method to identify coding variants by accurately sequencing even the most difficult genomic regions. Exome sequencing analyzes the protein-coding region of the genome, as a cost-effective alternative to whole-genome sequencing. The NextSeq 550 System can sequence 3–12 exomes per run. 

See how researchers use exome sequencing with the NextSeq 550 System:

HLA genetics and autoimmune disease

Cancer biomarker discovery

NextSeq 550 exome application note


The NextSeq 550 System sequences up to 384 small genomes per run to provide a detailed view of the genomes of the smallest organisms. Small whole-genome sequencing (WGS) enables comprehensive analysis of microbial or viral genomes for applications in public health, infectious disease surveillance, molecular epidemiology studies, and environmental metagenomics. 


More applications and methods

Amplicon sequencing

Perform ultra-deep sequencing of PCR amplicons with cost-effective analysis of up to hundreds of target genomic regions in one assay.

Methylation sequencing

Enhance epigenetic studies with high-coverage density and flexibility enabled by sequencing-based DNA methylation analysis.

Coding transcriptome analysis

Detect both known and novel features of the coding transcriptome using sequence-specific capture of RNA coding regions.

Microarray scanning

Scan Illumina microarrays with rapid, sensitive, and accurate imaging for exceptional genetic analysis.

Cytogenetic microarrays and sequencing

Perform sequencing and high-quality cytogenomic array-based analysis on a single platform for a range of constitutional and cancer research applications.

miRNA and small RNA analysis

Isolate and sequence small RNA species, such as microRNA, to study the role of noncoding RNA in gene silencing and posttranscriptional regulation. 

De novo sequencing

Enable fast, accurate characterization of novel genomes with no reference sequence available for any species.

RNA drug response biomarker discovery

Discover and profile RNA-based drug response biomarkers to help improve the efficiency and success rate of drug development.


Analyze protein interactions with DNA for genome-wide surveys of gene regulation.

Target enrichment

Use sequence-specific hybridization to analyze genomic regions of interest.

Genotyping by sequencing

Discover novel plant and animal SNPs and perform genotyping studies with a low-cost genetic screening method.

Targeted DNA sequencing

Focus time, expenses, and analysis on sequencing only a subset of genes or genome regions of research interest.


Assess genes in organisms present in a complex sample to evaluate bacterial diversity and detect unculturable microorganisms.

Translation analysis

Monitor cellular translation processes and determine what regions of a message are being translated with ribosome profiling.

Methylation arrays

Interrogate CpG sites at single-nucleotide resolution to get valuable insights into the regulation of gene expression.

Total RNA sequencing

Analyze coding RNA plus multiple forms of noncoding RNA for a comprehensive picture of the transcriptome. 

How others use this instrument

See what’s possible with the flexible NextSeq 550 System