Benchtop sequencers

Bring the power of NGS to your lab with easy-to-use platforms

NovaSeq 2000 in lab setting

Benchtop sequencing blends simplicity, performance

Benchtop sequencers give users the power of next-generation sequencing (NGS) in a flexible and accessible design. Built with operational simplicity including preconfigured analysis workflows, these systems enable novice and experienced NGS users to bring NGS in-house and perform targeted sequencing across a range of applications.

A benchtop sequencer can provide a cost-efficient solution for low and mid-throughput applications and for library quality control (QC) prior to large-scale studies.

scientist using NextSeq 2000

Take control of your sequencing

For users that are outsourcing their sequencing projects, investing in a benchtop sequencer to bring NGS in-house can offer several advantages:

  • Lower the cost of sequencing per sample
  • Shorten turnaround time to get results faster
  • Maintain control and privacy of your data

Types of benchtop sequencers

Depending on your needs, benchtop sequencers feature low- or mid-throughput configurations to support a broad range of applications while delivering exceptional data quality and accuracy.

Low-throughput benchtop system

Output: 15 megabases (Mb) to 50 gigabases (Gb)
Reads per run: 1 million to 40 million

  • Ideal for targeted sequencing at low to mid throughputs
  • Fast workflow for targeted samples
  • Well suited for pilot studies and library QC prior to larger projects

Mid-throughput benchtop system

Output: 10 Gb to 540 Gb
Reads per run: 75 million to 1.8 billion

  • Flexibility for wide range of emerging applications like spatial analysis and single-cell sequencing
  • Broader output range while maintaining a benchtop footprint
  • May include secondary analysis pipelines on-instrument

Find the right benchtop sequencer

Key factors to consider when looking to purchase a benchtop sequencing system include what applications your lab will use most and how you will analyze the data you generate.

Match data output to applications and sample number

Your methods and applications help determine if you need a low- or mid-throughput benchtop sequencer. If you’re primarily interested in small whole-genome, microbial metagenomics, and targeted gene sequencing, a low-throughput benchtop sequencer would be a good fit. For methods like whole-exome and single-cell, consider a mid-throughput benchtop sequencer.

Decide how you will analyze your data

Your goals for analysis are an important consideration when choosing a sequencing platform. Novice users may benefit from user-friendly, preconfigured analysis pipelines available on-instrument or in the cloud. For experienced users, you can take advantage of instrument compatibility with broader informatics pipelines or build your own.

Featured Illumina benchtop sequencers

Whether your lab is acquiring its first NGS sequencer, or is ready to scale up, Illumina offers proven benchtop sequencers with simplified operation, flexible and scalable sequencing, and intuitive data analysis. Straightforward, thoughtful design that includes onboard cluster generation and minimal maintenance sets these sequencers apart.

MiSeq System

The MiSeq System has a simplified NGS workflow making it easy for novice users to access NGS, quickly and reliably. With more than 10,000 systems shipped globally, the MiSeq System has the largest benchtop system install base on the market. Cited in over 100,000 peer-reviewed publications,1 it has been trusted for over a decade.

NextSeq 1000 and NextSeq 2000 Systems

The NextSeq 1000 and NextSeq 2000 Sequencing Systems are flexible and scalable, empowering scientists to explore applications like single cell, whole-exome, and RNA sequencing. With more than 2150 systems shipped globally, they feature simplified run setup, minimal touchpoints, and flexible informatics solutions, including onboard DRAGEN software.

Compare Illumina benchtop sequencing systems

Key specifications

iSeq 100 System

MiniSeq System

MiSeq System

NextSeq 1000 and 2000 Systems

Max output per flow cell (range) 144 Mb-1.2 Gb 1.65-7.5 Gb 540 Mb-15 Gb 10-540 Gb
Number of kit configurations 1 5 8 14
Run time (range) 9.5 - 19 hr 5 - 24 hr 5 - 56 hr 8 - 44 hr
Max reads per run (single reads) 4M 25M 25M 1.8B
Max read length 2 × 150 bp 2 × 150 bp 2 × 300 bp 2 × 300 bp
Key application
Supported application

*Small targeted panels < 50 genes, Large targeted panels > 50 genes

Key applications
Small whole-genome sequencing

(microbe, virus)

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

Key application
Key application
Key application
Targeted DNA sequencing

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

Key application with small targeted panels*

Key application with small targeted panels*

Key application with small targeted panels*

Key application with small targeted panels*

mRNA sequencing

Sensitive, accurate measurement of gene expression, after mRNA enrichment using poly-A capture.

Key application
Total RNA sequencing

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

Suppoted application
Key application
16s rRNA sequencing

A culture-free method to identify and compare bacteria from complex microbiomes or environments that are difficult to study.

Key application
Key application
Whole-exome sequencing

DNA technique analyzing coding regions of genes to identify genetic variants.

Key application
Metagenomic profiling

(shotgun metagenomics, metatrascriptomics)

Sequence thousands of organisms in parallel. Identify unculturable or low-abundance microbes, or evaluate microbial diversity.the entire genome of a bacterium, virus, or other microbe.

Key application

A popular method for determining chromatin accessibility across the genome.

Key application
Methylation sequencing

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

Key application
Targeted proteomics

Analyzes specific proteins to understand their function and interaction in biological systems.

Key application
Single-cell sequencing

Discovery of distinct cellular niches that comprise a larger tissue.

Key application
Spatial analysis

Obtain a comprehensive map of transcriptional activity within tissue sections.

Key application
Liquid biopsy research

Examine cell-free circulating tumor DNA as a noninvasive cancer biomarker.

Supported application
Immune repertoire sequencing

Decodes immune cell receptors to understand immune system diversity and response.

Key application
Key application
Large whole-genome sequencing


Extensive sequencing of entire genome.

Supported application

Explore iSeq 100 System


Explore MiniSeq System


Explore MiSeq System


Explore NextSeq 1000 and 2000 Systems


Confidently bring NGS to your lab with proven technology and support

When determining the best benchtop sequencer for your lab, it is important to select a vendor with a record of excellence. At Illumina, we continue our pursuit of innovation to inspire scientists to join our growing genomics community, and our proven performance has contributed to Illumina being cited more than any other sequencing company.

421,000+ Sequencing publications1
10,000+ MiSeq Systems placed worldwide
2150+ NextSeq 1000 and NextSeq 2000 Systems placed worldwide
3000+ Trainings per year
24/5 Remote technical support
150+ Countries served

Hear from the scientific community

In these videos and articles, hear from others about their experience with Illumina benchtop sequencing systems.

Seeking the source of baterial drug resistance

In this article, Dr Philip Supply explains how he uses the MiSeq System to evaluate patterns of extensive resistance, transmission, and evolution to identify multidrug-resistant tuberculosis strains responsible for silent outbreaks.

Speak with a specialist

Reach out for information about our products and services, or get answers to questions about our technology.


  1. Data calculations on file, Illumina, Inc. 2023.