Illumina MiniSeq

MiniSeq is a sequencer released by Illumina in January 2016. It is based on Sequencing by Synthesis (SBS).

Illumina MiniSeq
Photo of MiniSeq: by Illumina

MiniSeq is available in the following models:
  • MiniSeq High-Output
  • MiniSeq Mid-Output
  • MiniSeq Rapid


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date January 2016
Price [2] $49,500
MSRP as of March 2024
Type Benchtop
Weight 45 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina MiniSeq High-Output: 1x75bp to 2x150bp
Illumina MiniSeq Mid-Output: 2x150bp
Illumina MiniSeq Rapid: 1x100
Run time Illumina MiniSeq High-Output: 7 hours to 24 hours
Illumina MiniSeq Mid-Output: 17 hours
Illumina MiniSeq Rapid: 5 hours
Reagent cost per Gb [1] Illumina MiniSeq High-Output: $268.27
Illumina MiniSeq Mid-Output: $298.75
Illumina MiniSeq Rapid: $612.50
Data quality [3] Illumina MiniSeq High-Output: > 85% bases higher than Q30
Illumina MiniSeq Mid-Output: > 80% bases higher than Q30
Illumina MiniSeq Rapid: > 85% bases higher than Q30
Maximum output per run (Gb)[4] Illumina MiniSeq High-Output: 7.50
Illumina MiniSeq Mid-Output: 2.40
Illumina MiniSeq Rapid: 2.00
Primary error type [5] Substitutions
Notes about the specifications

  1. Cost per Gb: The cost per Gb is calculated by dividing the costs of sequencing reagents by the manufacturer’s maximum output per run. For these runs, the manufacturer may have included their own controls and used specific library preparation kits. Actual performance may vary based on sample and library type and quality, loading concentration, and other experimental factors. The sequencing reagent costs used for calculations do not include any other costs associated with preparing the samples or running the instrument, including reagents used for extraction, quality control or library preparation, labor, electricity, lab consumables, storage, etc. Performance metrics and prices are subject to change.
  2. Price: The final price may be different depending on the supplier, the region and any discounts provided through bulk orders or negotiation. Other factors that may influence the final price are warranty options, maintenance contracts, possible trade-ins of older instruments, and any financing arrangements chosen.
  3. Data quality: This is the maximum data quality that the instrument can offer based on manufacturer’s specifications and optimizations. The quality of a specific run will depend on multiple factors, including sample quality, sample quantity, library prep protocol, run conditions, etc.
  4. Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
  5. Primary error type: This is the most common type of error that may occur due to sequencing. Other types of error may occur as well.

More about the MiniSeq

The Illumina MiniSeq System is a benchtop next-generation sequencing (NGS) platform designed to bring the power of NGS into smaller, more focused research laboratories. It targets the segment of the NGS market prioritizing accessibility, ease of use, and rapid turnaround times for targeted sequencing projects. The MiniSeq can be seen as a successor to the popular MiSeq instrument, offering streamlined workflows and smaller output, better suited for the needs of certain labs.

Key Innovations

  • Simplified Workflow: The MiniSeq prioritizes a 'load-and-go' mentality, minimizing hands-on time and user intervention compared to larger Illumina sequencers. Ready-to-use reagent cartridges eliminate the need for manual preparation steps, reducing the risk of errors and inconsistencies. An intuitive touchscreen interface guides users through the run setup process, further streamlining operation. This simplified workflow makes the MiniSeq accessible to researchers with limited NGS experience and reduces overall time investment for experienced users.
  • Onboard Data Analysis: The MiniSeq integrates basic data analysis directly on the instrument. This eliminates the need for researchers to transfer raw sequence data to a separate computer or server for initial quality control (QC) metrics. After sequencing is complete, the MiniSeq automatically generates reports including key metrics like base calling accuracy and read quality scores. Having these results readily available allows researchers to assess data quality and make informed decisions about downstream analyses, all within the context of the sequencing run itself. While the onboard software doesn't replace the need for dedicated bioinformatic analysis for complex projects, it offers a valuable timesaving advantage for targeted sequencing applications where researchers primarily need to confirm successful library preparation and sequencing.
  • Rapid Turnaround Time: Run times on the MiniSeq can be completed in a single workday, often within as little as 12 hours. This rapid turnaround time is ideal for researchers who need answers quickly, whether to inform critical decisions within an ongoing experiment or to expedite the publication process. The MiniSeq's ability to generate sequencing data overnight allows researchers to make the most of their lab time and adapt their research strategies as needed based on the results.

Features and Technologies

  • Sequencing Chemistry: The MiniSeq utilizes Illumina's proven Sequencing-by-Synthesis (SBS) chemistry. This ensures high accuracy and familiar data output for researchers already in the Illumina ecosystem.
  • Flexible Run Output: Several run kits are available, with options producing up to 25 million reads, suitable for various targeted sequencing applications.
  • Compact Footprint: The MiniSeq's benchtop size maximizes usability in labs with limited space.
  • Accuracy: The MiniSeq maintains the high accuracy standards of Illumina SBS.
  • Read Lengths: The MiniSeq supports paired-end reads up to 150 bases in length.

Intended Uses and Specific Applications

The MiniSeq excels in applications requiring targeted or small-genome sequencing. Examples include:

  • Amplicon Sequencing: Amplicon sequencing allows researchers to target and amplify specific regions of DNA or RNA.
  • 16S rRNA Sequencing: By sequencing the 16S ribosomal RNA gene, researchers can profile the bacterial and archaeal communities within a sample.
  • Small RNA Sequencing: Small RNAs, such as microRNAs (miRNAs) and small interfering RNAs (siRNAs), are important regulators of gene expression.
  • Small Genome Sequencing: The MiniSeq can be used for sequencing of the complete genomes of small organisms, such as bacteria and viruses.
  • Targeted Sequencing: Targeted resequencing allows researchers to focus on specific regions of a genome for variant discovery.

Comparison with Competing Instruments

  • Ilumina iSeq 100: The iSeq 100 has even smaller output but faster run times on average than the MiniSeq. Choose the iSeq 100 for ultra-rapid results on very small projects.
  • Illumina MiSeq: The MiSeq offers higher maximum output per run with longer available read lengths than the MiniSeq, although the MiSeq run times are longer. Choose the MiSeq for greater output flexibility or if the simplified MiniSeq workflow isn't essential.
  • Complete Genomics DNBSEQ-E25: The DNBSEQ-E25 is very similar to the MiniSeq, as they both can offer read lengths as long as 2x150 bp, quick run times and the same max output per run. However, the MiniSeq offers more variability with its reagent kits and uses different technology than the DNBSEQ-E25.

Special Considerations

The MiniSeq is an excellent option for researchers and labs who:

  • Prioritize ease of use and fast turnaround times over maximum sequencing output.
  • Are new to NGS or have limited bioinformatics resources. Onboard analysis can be a major advantage.
  • Focus on routine, targeted sequencing applications where the MiniSeq's output range and simplified workflow are well-aligned.

Need sequencing done on a Illumina MiniSeq or a specific instrument? Tell us about your project here, and we'll connect you with a qualified provider.

This information on this page is up-to-date as of April 23, 2024 and based on the spec sheets published by the manufacturer.