Illumina HiSeq X

HiSeq X is a sequencer released by Illumina in January 2014. It is based on Sequencing by Synthesis (SBS).

Illumina HiSeq X
Image of HiSeq X: by Illumina


Manufacturer Illumina
Technology Sequencing by Synthesis (SBS)
Release date January 2014
Price [2] $1,000,000
Estimated MSRP as of the release date. Illumina would only sell them as a bundle of 5 (HiSeq X Five) or bundle of 10 (HiSeq X Ten).
Type Industrial
Weight 225.9 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ
Read length Illumina HiSeq X: 2x150bp
Run time Illumina HiSeq X: 72 hours
Reagent cost per Gb [1] Illumina HiSeq X: Unavailable
Data quality [3] Illumina HiSeq X: ≥ 75% of bases above Q30
Maximum output per run (Gb)[4] Illumina HiSeq X: 180.00
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 HiSeq X

The Illumina HiSeq X Series, launched in 2014, was designed as a successor to the HiSeq 2500, offering a significant increase in data output and reduction in cost per genome sequenced. It should be noted that Illumina has discontinued the HiSeq X and has chosen to focus on developing instruments with improved throughput and capabilities, such as the NovaSeq series.

Key Innovations

The HiSeq X series introduced patterned flow cells, which contained billions of nanowells at specific locations and increased the density of sequencing lanes compared to previous models. This, coupled with advancements in sequencing chemistry, enabled the HiSeq X Ten (a configuration with 10 HiSeq X instruments) to achieve a dramatic increase in data output – capable of generating up to 1.8 terabases of data per run, enough for 16 human whole genomes at 30X coverage.

Features and Technologies

The HiSeq X boasted several improvements compared to its predecessors:

  • Ultra-high throughput: As mentioned earlier, the HiSeq X Ten enabled population-scale whole genome sequencing (WGS) by delivering up to 18,000 human genomes per year at 30X coverage.
  • Reduced cost per genome: Illumina's goal with the HiSeq X was to achieve the $1,000 human genome, and while the actual costs per genome might have varied depending on service providers and project specifics, the HiSeq X significantly brought down the cost barrier for large-scale WGS projects.
  • Scalability: Labs could purchase the HiSeq X Five system first and then scale up to the HiSeq X Ten later once they needed to upgrade their sequencing capacity.
  • Data Quality: The HiSeq X delivered high-quality data with Illumina's established sequencing-by-synthesis technology. The platform achieved base qualities exceeding Q30 (accuracy greater than 99.9%) for a significant portion of reads.

Intended Uses and Specific Applications

The primary application of the HiSeq X was large-scale whole genome sequencing projects, particularly in population genetics and human disease research. It was not suitable for other applications such as RNA-Seq, exome sequencing, or ChIP-Seq. Additionally, Illumina initially restricted its use to human samples, although this was later expanded to other species.

Suitable Illumina library prep kits included the TruSeq DNA PCR-Free and TruSeq Nano DNA Library Preparation kits.

Comparison with Competing Instruments

Here's a comparison of HiSeq X with competing instruments offering similar throughput:

  • Illumina NovaSeq 6000: Launched after the HiSeq X, the NovaSeq series offers comparable run throughput at faster speeds and is suitable for a variety of applications, not just whole genome sequencing.
  • PacBio Onso: Designed for short-read sequencing, the PacBio Onso offers a similar data output to 1 lane of the HiSeq X but with a different technology. The PacBio Onso utilizes sequencing by binding (SBB) chemistry, sequencing, which generates similar read lengths to Illumina but at higher accuracy. The Onso is also suitable for a variety of applications, although the HiSeq X may be the better choice for high-output whole genome sequencing projects.*
  • Singular Genomics G4: This platform offers similar throughput to 1 lane of the HiSeq X and is suitable for a variety of applications at a low upfront cost. However, for high-output whole genome sequencing, the HiSeq X is the better choice.*

*Note: The HiSeq X is discontinued, so it’s availability has drastically reduced. This should be taken into account when comparing it to other instruments.

Special Considerations

Choosing the right sequencing platform depends on your specific research needs and budget. Here are some factors to consider when evaluating the HiSeq X:

  • Project scope: If your project involves large-scale whole genome sequencing of human or other species, the HiSeq X can be a cost-effective option.
  • Sequencing needs: If your project requires targeted sequencing applications like RNA-Seq or exome sequencing, the HiSeq X is not suitable.
  • Budget: While the HiSeq X offered a significant reduction in sequencing costs compared to previous instruments, the upfront instrument cost and ongoing reagent expenses need to be factored into your budget considerations. Newer instruments might offer similar or better performance at potentially lower costs.
  • Discontinuation: It's important to note that the HiSeq X has been discontinued and Illumina is no longer providing full support of the instruments as of April 1, 2024. This could impact the long-term availability of reagents and service support for the platform.

Need sequencing done on a Illumina HiSeq X 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.