Illumina iSeq 100

iSeq 100 is a sequencer released by Illumina in January 2018. It is based on Sequencing by Synthesis (SBS).

Illumina iSeq 100
Image of iSeq 100: by Illumina


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date January 2018
Price [2] $19,900
MSRP as of March 2024
Type Benchtop
Weight 15.9 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina iSeq 100: 1x36bp to 2x150bp
Run time Illumina iSeq 100: 9.5 to 19 hours
Reagent cost per Gb [1] Illumina iSeq 100: $536.67
Data quality [3] Illumina iSeq 100: > 85% of bases higher than Q30
Maximum output per run (Gb)[4] Illumina iSeq 100: 1.20
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 iSeq 100

The Illumina iSeq 100 is a compact and affordable benchtop sequencer designed for smaller labs or targeted sequencing applications. It fills a specific niche in the next-generation sequencing (NGS) market by providing fast, accessible, and high-quality data for projects that don't require the throughput of larger production-scale sequencers. The iSeq 100 maintains the accuracy and reliability associated with Illumina's sequencing by synthesis (SBS) chemistry.

Key Innovations

  • CMOS Sensor Technology: The iSeq 100 sets itself apart by utilizing a complementary metal-oxide semiconductor (CMOS) image sensor chip, similar to those found in smartphone cameras. This chip is paired with a specialized one-channel SBS chemistry designed for optimal signal detection. By replacing conventional laser optics and camera systems, the CMOS sensor design simplifies the instrument significantly, reduces instrument cost and results in a smaller footprint, while still delivering accurate data.
  • Simplified Workflow: The iSeq 100 boasts a streamlined setup and operation process. Prefilled reagent cartridges and an intuitive software interface minimize hands-on time, making NGS accessible to labs without dedicated sequencing specialists.

Features and Technologies

  • Sequencing by Synthesis (SBS): The iSeq 100 employs Illumina's proven SBS chemistry, using fluorescently labeled nucleotides to generate highly accurate sequencing data.
  • Single-Lane Flow Cell: The iSeq 100's flow cell has a single sequencing lane, optimized for smaller output runs.
  • Data Output: Capable of producing up to 1.2 Gb of data per run.
  • Run Time: Sequencing runs can be completed in 19 hours or less.
  • Read Length: Supports up to 2 x 150 bp (paired-end) reads.

Intended Uses and Specific Applications

The iSeq 100's capabilities make it ideal for various research applications, including:

  • Small Whole-Genome Sequencing: Sequencing of smaller genomes like bacteria, viruses, and plasmids. Suitable library prep kits include Illumina DNA Prep Library Prep Kit or Nextera XT DNA Library Prep Kit.
  • Targeted Gene Sequencing: Analysis of specific genes or regions of interest (panels). Suitable kits include TruSight One Panels or AmpliSeq Custom Panels.
  • Gene Expression Profiling: Measuring RNA expression using kits like Illumina Stranded mRNA Prep.
  • 16S Metagenomics: Characterization of microbial communities. Suitable library prep includes Illumina DNA Prep Library Prep Kit or the Illumina 16S Metagenomic Sequencing Protocol.

Comparison with Competing Instruments

  • Illumina MiniSeq: The MiniSeq offers higher throughput (up to 7.5 Gb per run). It's a better choice for projects requiring larger sequencing output, but it comes with increased instrument cost and complexity.
  • Complete Genomics DNBSEQ-E25: This platform offer higher max output and similar speeds, but it cannot offer the shorter sequencing read lengths available to the iSeq 100 and may come at a higher upfront cost.

Special Considerations

The iSeq 100 is a compelling option when these factors are important:

  • Ease of Use: Ideal for labs that want reliable NGS data without the complexity or in-house expertise requirements of larger sequencing platforms.
  • Affordability: Offers a lower initial investment compared to larger Illumina sequencers or comparable competitors.
  • Fast Turnaround Time: Delivers results quickly when time is a critical factor.

Need sequencing done on a Illumina iSeq 100 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 11, 2024 and based on the spec sheets published by the manufacturer.