Ion Torrent Genexus System

Genexus System is a sequencer released by Thermo Fisher Scientific in December 2019. It is based on Ion Torrent Semiconductor Sequencing.

Ion Torrent Genexus System
Image of Genexus: by ThermoFisher Scientific

Genexus System is available in the following models:
  • GX5 Chip
  • GX7 Chip


Manufacturer Thermo Fisher Scientific
Technology Ion Torrent Semiconductor Sequencing
Release date December 2019
Price [2] $299,000
MSRP as of release date
Type Benchtop
Weight 204.1 Kg
Supports real-time analysis No
Demultiplexing support Yes
File format FASTQ, SFF, BAM, and VCF
Read length Ion Torrent GX5 Chip: Up to 400bp
Ion Torrent GX7 Chip: Up to 200bp
Run time Ion Torrent GX5 Chip: 14 to 24 hours
Ion Torrent GX7 Chip: 14 to 24 hours
Reagent cost per Gb [1] Ion Torrent GX5 Chip: $273.83
Ion Torrent GX7 Chip: $82.15
Data quality [3] Ion Torrent GX5 Chip:
Ion Torrent GX7 Chip:
Maximum output per run (Gb)[4] Ion Torrent GX5 Chip: 6.00
Ion Torrent GX7 Chip: 20.00
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 Genexus System

The Genexus System, developed by Thermo Fisher Scientific and released on 2019, falls within the benchtop next-generation sequencing (NGS) market segment. It targets labs seeking a user-friendly platform for automated NGS workflows, particularly those with moderate throughput requirements. While not a direct successor, it offers a more streamlined and automated alternative to earlier Ion Torrent instruments like the PGM and Proton.

Key Innovations

The core innovation of the Genexus System lies in its walk-away automation, significantly reducing hands-on time and minimizing errors throughout the NGS workflow. The system comprises two integrated instruments: the Genexus Purification System and the Genexus Integrated Sequencer. These work seamlessly together, orchestrated by the intuitive Genexus software, to handle all critical steps – from nucleic acid extraction, purification and quantification to library preparation, sequencing, and even preliminary data analysis. This automation eliminates the need for manual intervention in complex and error-prone procedures like library construction, a well-known bottleneck in NGS. By automating these steps, the Genexus System ensures consistency and reproducibility across runs, a crucial aspect for generating reliable NGS data.

Features and Technologies

The Genexus System boasts several user-friendly features:

  • Pre-loaded cartridges: Reagent cartridges containing all necessary components eliminate the need for manual preparation and mixing, reducing variability and saving time.
  • Sample tracking: Barcoded samples and reagents ensure traceability throughout the workflow.
  • Simplified run setup: Automated protocols and software guidance streamline experiment setup.
  • Onboard data analysis: Preliminary data analysis tools allow for quick data assessment at the instrument.
  • Quick turnaround time: The system delivers results in as little as 24 hours, making it suitable for time-sensitive applications.

Intended Uses and Specific Applications

The Genexus System caters to a wide range of NGS applications, including:

  • Targeted Sequencing: Identify mutations in specific genes associated with diseases or traits using Ion AmpliSeq technology.
  • Amplicon sequencing: Investigate specific regions of the genome, such as the 16S rRNA gene for bacterial identification or targeted regions for variant analysis, by amplifying and sequencing these regions using Ion AmpliSeq HD technology.

Comparison with Competing Instruments

  • Ion Torrent GeneStudio S5: Offers longer possible read lengths and higher max output at faster run times. However, it requires more hands-on operation compared to Genexus.
  • Illumina NextSeq 550: The NextSeq 550 is similar in upfront price and run time range while offering much higher max output. However, its read lengths are shorter than the Genexus, and Illumina reagents tend to be more expensive than Thermo Fisher sequencing reagents.
  • Complete Genomics DNBSEQ-G99: The DNBSEQ-G99 offers faster run times and higher max output, but the Genexus can reach longer read lengths.

Special Considerations

The Genexus System is a compelling option for labs seeking several key advantages:

  • Ease of Use and Automation: The walk-away automation minimizes hands-on time and user expertise required for NGS, making it suitable for labs with limited NGS experience or for integrating NGS into routine workflows.
  • Standardization and Reproducibility: The automated workflows and pre-filled cartridges ensure consistency across runs, minimizing technical variations and generating reliable data.
  • Fast Turnaround Time: The ability to deliver results in as little as 24 hours makes the Genexus System ideal for time-sensitive applications where rapid turnaround is critical.
  • Moderate Throughput: While not the highest throughput instrument, the Genexus System offers sufficient capacity for many research projects and clinical applications with moderate sequencing needs.

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This information on this page is up-to-date as of May 8, 2024 and based on the spec sheets published by the manufacturer.