NextSeq 1000 & NextSeq 2000 Applications & Methods

Key Applications and Methods

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Efficient and Cost-Effective

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

More Applications and Methods*

Small Whole-Genome Sequencing

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

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.

Target Enrichment

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

Total RNA Sequencing

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

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.

*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.

NextSeq 1000 and NextSeq 2000: A Range of Applications

The NextSeq 1000 and NextSeq 2000 Systems offer an intuitive workflow with load-and-go ease, on-board informatics, and flexibility to run many NGS applications. Register to see a virtual instrument demo and learn more about these solutions enabled by our newest platform, followed by open audience Q&A.

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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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