NextSeq 1000 & NextSeq 2000 Applications & Methods

Key Applications and Methods

More Applications and Methods*

Spatial Transcriptomics

By retaining the precise location of biological molecules within a tissue, spatial methods can further our understanding of mechanisms in health and disease.

ctDNA Sequencing

Next-generation sequencing offers the sensitivity and specificity that researchers need to detect low levels of circulating tumor DNA in the bloodstream.

Shotgun Metagenomic Sequencing

Sequence thousands of organisms in parallel. Identify unculturable or low-abundance microbes, or evaluate microbial diversity.

Small Whole-Genome Sequencing

Sequence the entire genome of a bacterium, virus, or other microbe.

Target Enrichment

Capture genomic regions of interest via hybridization to target-specific biotinylated probes.

Targeted RNA Sequencing

Select and sequence specific transcripts of interest for gene expression profiling studies.

Methylation Sequencing

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


Chromatin immunoprecipitation sequencing (ChIP-Seq) is a powerful method for analyzing DNA-protein interactions and performing genome-wide surveys of gene regulation.


The assay for transposase-accessible chromatin with sequencing (ATAC-Seq) is a popular method for determining chromatin accessibility across the genome.

Amplicon Sequencing

Ultra-deep sequencing of PCR amplicons enables cost-effective analysis of up to hundreds of target genomic regions in one assay.

Targeted Gene Panels

Targeted gene sequencing panels are useful tools for analyzing specific mutations in a given sample.

Total RNA Sequencing

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

16S Metagenomic Sequencing

Sequencing the 16S ribosomal RNA (rRNA) gene is a culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.

Immune Repertoire Analysis

Identify unique receptor variants to map the vast repertoire of immune cells that are capable of recognizing a seemingly boundless array of targets.

*The NextSeq 1000 and NextSeq 2000 Systems are scalable platforms that can support a broad range of current and emerging applications beyond those listed here.

Multiomics Multiplies Your Discovery Power

The P3 flow cell on the NextSeq 2000 is an excellent fit for multiomics studies. Use multiomics to better connect genotype to phenotype and obtain a full cellular readout not found through single multiomics approaches.

Learn About Multiomics at a Glance

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Hear from Fellow Researchers

Researchers discuss their experience using the
NextSeq 1000 and NextSeq 2000 Sequencing Systems.

NextSeq 2000: A Range of Applications

Learn how the NextSeq 2000 system delivers the flexibility to support your research needs including bulk RNA-Seq, target enrichment, single-cell RNA Seq and much more.

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Publication Reviews

These summaries of peer-reviewed publications highlight how Illumina technology is furthering research.


Ask virtually any question related to the genome, transcriptome, or epigenome of any organism. Explore a broad range of NGS methods.

Illumina Resources & Tools

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