Ion Torrent GeneStudio S5 System

GeneStudio S5 System is a sequencer released by Thermo Fisher Scientific in June 2018. It is based on Ion Torrent Semiconductor Sequencing.

Ion Torrent GeneStudio S5 System
Image of GeneStudio S5: https://www.thermofisher.com/order/catalog/product/A44671 by ThermoFisher Scientific

GeneStudio S5 System is available in the following models:
  • GeneStudio S5
  • GeneStudio S5 Plus
  • GeneStudio S5 Prime
  • S5/S5 XL 520 Chip
  • S5/S5 XL 530 Chip
  • S5/S5 XL 540 Chip

Specifications

Manufacturer Thermo Fisher Scientific
Technology Ion Torrent Semiconductor Sequencing
Release date June 2018
Price [2] $75,500
MSRP as of March 2024
Type Benchtop
Weight 63.5 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ, SFF, BAM, and VCF
Read length Ion Torrent GeneStudio S5: 200bp to 600bp
Ion Torrent GeneStudio S5 Plus: 200bp to 600bp
Ion Torrent GeneStudio S5 Prime: 200bp to 600bp
Ion Torrent S5/S5 XL 520 Chip: 200bp to 600bp
Ion Torrent S5/S5 XL 530 Chip: 200bp to 600bp
Ion Torrent S5/S5 XL 540 Chip: 200bp
Run time Ion Torrent GeneStudio S5: 4.5 to 21.5 hours
Ion Torrent GeneStudio S5 Plus: 3 to 20 hours
Ion Torrent GeneStudio S5 Prime: 3 to 12 hours
Ion Torrent S5/S5 XL 520 Chip: 3 to 12 hours
Ion Torrent S5/S5 XL 530 Chip: 4 to 21.5 hours
Ion Torrent S5/S5 XL 540 Chip: 6.5 to 20 hours
Reagent cost per Gb [1] Ion Torrent GeneStudio S5: $56.93
Ion Torrent GeneStudio S5 Plus: $56.93
Ion Torrent GeneStudio S5 Prime: $34.16
Ion Torrent S5/S5 XL 520 Chip: Unavailable
Ion Torrent S5/S5 XL 530 Chip: Unavailable
Ion Torrent S5/S5 XL 540 Chip: Unavailable
Data quality [3] Ion Torrent GeneStudio S5: >99% aligned/measured accuracy
Ion Torrent GeneStudio S5 Plus: >99% aligned/measured accuracy
Ion Torrent GeneStudio S5 Prime: >99% aligned/measured accuracy
Ion Torrent S5/S5 XL 520 Chip: >99% aligned or measured accuracy
Ion Torrent S5/S5 XL 530 Chip: >99% aligned or measured accuracy
Ion Torrent S5/S5 XL 540 Chip: >99% aligned or measured accuracy
Maximum output per run (Gb)[4] Ion Torrent GeneStudio S5: 15.00
Ion Torrent GeneStudio S5 Plus: 30.00
Ion Torrent GeneStudio S5 Prime: 50.00
Ion Torrent S5/S5 XL 520 Chip: 2.00
Ion Torrent S5/S5 XL 530 Chip: 8.00
Ion Torrent S5/S5 XL 540 Chip: 30.00
Primary error type [5] Indels
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 GeneStudio S5 System

The Ion GeneStudio S5 (S5) System is a benchtop next-generation sequencing (NGS) platform from Thermo Fisher Scientific designed for targeted sequencing applications. Released in 2018, it falls under the category of semiconductor-based sequencers, a sub-segment known for its speed and affordability compared to traditional sequencing methods. While no longer the most recent model (succeeded by the Ion Genexus), the S5 remains a relevant option for researchers due to its established user base, affordability, and ease of use.

Key Innovations

  • Scalable Output and Varied Run Times: The S5 leverages different models, which offer researchers a high degree of flexibility and scalability in terms of read output and run time. They are the S5, S5 Plus and S5 Prime Systems, and they are compatible with different chips and have different sequencing speeds. The low-capacity Ion Chips allow for cost-effective use of the instrument for smaller projects requiring only a few million reads. Conversely, the high-capacity Ion Chips enable researchers to generate up to 130 million reads in a single run, ideal for analyzing larger panels of genes or multiple samples simultaneously. The Plus and Prime systems are compatible with the higher output 550 Ion Chip with the Prime having the fastest run times.

Features and Technologies

  • Speed via Semiconductor Sequencing: The S5 system utilizes semiconductor sequencing technology, which translated chemically encoded information, like the identity of nucleotides, into digital information on a semiconductor chip. This enables rapid run times of under 6 hours, especially for low-output projects.
  • User-Friendly Design: The S5 incorporates cartridge-based reagents and a user-friendly interface, minimizing pre-run setup time and simplifying operation for researchers new to NGS.

Intended Uses and Specific Applications

The S5 system is particularly suited for targeted resequencing applications, including:

  • Amplicon sequencing: Targeted resequencing of specific gene panels or exomes using Ion AmpliSeq library prep kits.
  • Targeted metagenomics: Analysis of microbial communities through 16S rRNA gene sequencing with kits like the Ion 16S Metagenomics Kit.
  • HLA genotyping: High-resolution genotyping of human leukocyte antigen (HLA) genes for transplantation compatibility testing with kits like the AllType FASTplex assay.

Comparison with Competing Instruments

Here's a comparison of the S5 to other sequencing instruments in its throughput range:

  • Ion Torrent Genexus: Offers higher throughput at similar accuracy but comes with a larger footprint, higher upfront cost, and longer average run times than the GeneStudio S5.
  • Illumina MiSeq: A major competitor with comparable data quality but slightly lower max output. The MiSeq offers a broader range of library prep options with paired end reads, and Illumina offers different reagent kits for different needs (speed vs. output). However, the GeneStudio S5 still has shorter run times, especially at the higher output end, and its got a lower upfront cost.
  • DNBSEQ-E25: This sequencer boasts comparable fast run times, the option for paired ends, and the ability to be used in the field. However, the possible output is lower than the GeneStudio S5, especially taking into account the different available S5 models.

Special Considerations

The Ion Torrent GeneStudio S5 stands out as a compelling choice for targeted NGS workflows due to several factors:

  • Cost-effective targeted sequencing: The S5 offers a combination of affordable upfront costs and competitive reagent costs per run, making it a budget-friendly option for labs focused on targeted resequencing applications.
  • Speed: With average run times under 6 hours, the S5 delivers results significantly faster than some competing platforms, ideal for researchers needing rapid turnaround times.
  • Ease of use: The S5's user-friendly cartridge-based system and streamlined workflow minimize pre-run setup and make it manageable for labs with limited NGS experience.
  • Scalability: The S5 caters to projects of varying sizes with its interchangeable Ion Chip options, offering scalability without requiring a complete switch to a new platform.

Need sequencing done on a Ion Torrent GeneStudio S5 System 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 May 6, 2024 and based on the spec sheets published by the manufacturer.