MiniSeq Sequencing System

Let your work flow

Simple, accessible sequencing for targeted DNA and RNA applications

MiniSeq Sequencing System

Webster University experiences the MiniSeq System

Learn how professors at Webster University harness the easy-to-use MiniSeq System to unlock new research possibilities and foster faculty and student collaborations.

MiniSeq System in the lab
An affordable, accessible sequencing system

The MiniSeq System delivers the power and confidence of proven Illumina next-generation sequencing (NGS) technology in an accessible sequencing solution. The MiniSeq System features:

  • Cost-efficient sequencing, even for low numbers of samples
  • A streamlined workflow that enables rapid sequencing of both DNA and RNA
  • A small footprint that fits easily into laboratories, without specialized ancillary equipment
scientist using MiniSeq for NGS workflow
Simple library-to-results workflow

The MiniSeq System combines load-and-go operation with an intuitive user interface for a fast, easy NGS workflow. The MiniSeq System integrates clonal amplification, sequencing by synthesis, and base calling into a single benchtop tool, eliminating the need for additional equipment. Simply load the flow cell and reagent cartridge into the MiniSeq System and sequence at the touch of a button.

view of intuitive software onboard MiniSeq sequencing system
User-friendly, intuitive software

The MiniSeq System features a touch screen interface and user-friendly, intuitive software. Configure, launch, monitor, and analyze sequencing runs with onboard Local Run Manager. Interface with the MiniSeq System from any web browser to review real-time data and performance metrics. 

Perform secure analysis of MiniSeq System data in the cloud with BaseSpace Sequence Hub. Access accelerated bioinformatics with push-button tools, enabling you to easily analyze, archive, and share sequencing data. Optimized data analysis workflows are available for a growing ecosystem of applications.


An everyday tool for labs of any size

Examine single genes or entire pathways—all in a single run. Get efficient sequencing across a range of applications and sample quantities to help answer a myriad of research questions.

High-impact sequencing

MiniSeq instrument specifications 

System specifications

  • Output range
    1.65–7.5 Gb
  • Single reads per run
  • Max read length
    2 × 150 bp
  • Run time
    4–24 hr

A rapid, easy-to-learn workflow

Find insights with an integrated workflow requiring minimal hands-on time.

Prepare libraries

Prepare DNA or RNA libraries for a diverse range of targeted applications using optimized library prep kits.


Load and set up a run in < 5 minutes with an intuitive user interface and simple operation. Complete sequencing in < 1 day.

Analyze data

Configure, launch, monitor, and analyze sequencing runs using the onboard software suite.

Interpret results

Interface with the MiniSeq System from any web browser to review real-time data and performance metrics.

Flexible NGS for a range of applications

The MiniSeq System enables researchers to transition easily between sequencing projects for both DNA and RNA applications, including targeted resequencing, expression profiling, tumor profiling, germline mutation analysis, and more.

NGS library prep

Compare with other benchtop sequencing systems


MiniSeq System

iSeq 100 System

MiSeq System

Run time 4–24 hr 9–19 hr 5–55 hr
Maximum output per run 7.5 Gb 1.2 Gb 15 Gb
Maximum single reads per run 25Ma 4M 25Mb
Maximum read length 2 × 150 bp 2 × 150 bp 2 × 300 bp
Data analysis offeringsc BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server BaseSpace Sequence Hub, Illumina Connected Analytics, on-premises DRAGEN server

a. For MiniSeq High Output Reagent Kit only.

b. For MiSeq Reagent Kit v3 only.

c. A dedicated DRAGEN server is paired with an Illumina sequencing system and can be used to plan secondary analysis as part of a sequencing run using the Illumina Run Manager. An on-premises DRAGEN server does not communicate directly with the sequencing system but can ingest and process data from any Illumina sequencing system via a command-line.

Popular products

MiniSeq Reagent Kit

MiniSeq System Reagent kits have a ready-to-use cartridge with two-channel SBS chemistry for cost-efficient sequencing, even for low sample numbers.

TruSight Hereditary Cancer Panel

Targeted sequencing panel that assesses germline mutations across 113 genes and 125 SNPs associated with genetic cancer risk predisposition.

Urinary Pathogen ID/AMR Enrichment Kit

A library prep and enrichment kit that enables sensitive, culture-free detection and analysis of common and underrecognized uropathogens and AMR genes.

Speak with a specialist

Ready to speak to someone? Contact us to learn if the MiniSeq System is right for your research needs.