Oxford Nanopore GridION

Published on May 1, 2024

GridION is a sequencer released by Oxford Nanopore Technologies in January 2017. It is based on Nanopore Sequencing.

Oxford Nanopore GridION
Image of GridION: https://nanoporetech.com/products/sequence/gridion by Oxford Nanopore

GridION is available in the following models:

GridION with kit 10/11 chemistry
GridION with kit 12 chemistry
GridION with kit 14 chemistry

Specifications

Manufacturer	Oxford Nanopore Technologies
Technology	Nanopore Sequencing
Release date	January 2017
Price [2]	$70,000 MSRP as of March 2024
Type	Benchtop
Weight	11 Kg
Supports real-time analysis	Yes
Demultiplexing support	Yes
File format	FAST5
Read length	Oxford Nanopore GridION with kit 10/11 chemistry: typically 6-20 Kbp Oxford Nanopore GridION with kit 12 chemistry: typically 6-20 Kbp Oxford Nanopore GridION with kit 14 chemistry: typically 6-20 Kbp
Run time	Oxford Nanopore GridION with kit 10/11 chemistry: Up to 72 hours Oxford Nanopore GridION with kit 12 chemistry: Up to 72 hours Oxford Nanopore GridION with kit 14 chemistry: Up to 72 hours
Reagent cost per Gb [1]	Oxford Nanopore GridION with kit 10/11 chemistry: Unavailable Oxford Nanopore GridION with kit 12 chemistry: Unavailable Oxford Nanopore GridION with kit 14 chemistry: Unavailable
Data quality [3]	Oxford Nanopore GridION with kit 10/11 chemistry: Oxford Nanopore GridION with kit 12 chemistry: Oxford Nanopore GridION with kit 14 chemistry: > Q20 (99%) for Simplex reads, ~Q30 (99.9%) for Duplex reads
Maximum output per run (Gb)[4]	Oxford Nanopore GridION with kit 10/11 chemistry: 240.00 Oxford Nanopore GridION with kit 12 chemistry: 240.00 Oxford Nanopore GridION with kit 14 chemistry: 240.00
Primary error type [5]	Indels

Notes about the specifications

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.
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.
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.
Maximum output: This is the maximum output of a full instrument run. This number is based on manufacturer’s specifications and optimizations.
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 GridION

The Oxford Nanopore GridION, released in 2017, is a benchtop next-generation sequencing (NGS) system designed for researchers venturing into the realm of nanopore sequencing. Unlike short-read sequencers that dominate the NGS landscape, GridION specializes in generating long reads, offering distinct advantages for specific applications. While not a direct successor, the GridION builds upon the portability of the MinION, another nanopore sequencer from Oxford Nanopore, by providing a more robust platform for higher throughput sequencing in a lab setting.

Key Innovations

GridION's core innovation lies in its ability to run multiple nanopore sequencing experiments concurrently. The system boasts five independent flow cell ports, allowing researchers to launch up to five sequencing runs simultaneously. This parallel processing significantly boosts throughput compared to single-run sequencers, making GridION ideal for projects with numerous samples or larger genomes.

This feat is achieved through miniaturized flow cells called Flongles or the standard MinION flow cells. Each flow cell houses a nanopore array, essentially microscopic protein channels that biological molecules can traverse. By applying an electrical current, GridION detects disruptions in this current as DNA or RNA molecules pass through the nanopores, revealing the sequence of bases in real-time. The integrated high-performance computer within GridION performs basecalling, converting the raw electrical signal into a readable DNA or RNA sequence, for each nanopore simultaneously across all five flow cells.

Features and Technologies

GridION boasts several user-friendly features. The system requires minimal setup, making it accessible to researchers with limited NGS experience. The intuitive user interface streamlines experiment initiation and data acquisition. Most importantly, GridION eliminates the need for external compute resources by housing a powerful onboard computer for real-time basecalling and data processing. This translates to faster turnaround times and simplified data management.

In terms of data quality, GridION delivers long reads with raw read accuracy exceeding 99% > Q20. However, it's important to note that nanopore sequencing inherently has a higher error rate compared to short-read sequencing technologies. The strength of nanopore sequencing lies in the generation of ultra-long reads, the longest exceeding 4 Mb, which can be critical for specific applications.

Intended Uses and Specific Applications

GridION excels in applications that leverage the power of long reads. Here are a few prime examples:

De Novo Genome Assembly: For assembling genomes from scratch, particularly those of complex organisms with repetitive regions, long reads from GridION can help bridge gaps and generate more contiguous assemblies. An example of a suitable kit is the Nanopore Ligation Sequencing Kit.
Transcriptome Analysis: Long reads are crucial for capturing full-length transcripts, including isoforms, and for elucidating alternative splicing events. An example of a suitable kit is the Nanopore Direct RNA Sequencing Kit.
Metagenomics: Unraveling the complex composition of microbial communities can often require long reads to differentiate closely related species. An example of a suitable kit is the Nanopore Rapid Sequencing Kit.

Comparison with Competing Instruments

When selecting an NGS platform, researchers must consider a multitude of factors. Here's a quick comparison of GridION with its closest competitors:

Oxford Nanopore MinION: While offering similar read lengths and accuracy along with being portable and even more affordable, the MinION offers significantly lower throughput than the GridION with only one flow cell.
Oxford Nanopore PromethION: A true powerhouse in the nanopore sequencing world, the PromethION boasts ultra-high throughput with the ability to run dozens of flow cells simultaneously while still offering similar read lengths and accuracy compared to the GridION. However, the PromethION comes with a significantly higher upfront instrument cost and has larger footprint.
PacBio Revio: Another long-read sequencer, the PacBio Revio boasts higher data accuracy but generates shorter reads on average compared to GridION. The Revio also cannot perform real-time analysis, the upfront cost is much higher and the laboratory footprint is much larger than the GridION.

Special Considerations

GridION caters to researchers needing these specific advantages:

Moderately high throughput with long reads: If your projects involve multiple samples or larger genomes, but don't require the ultra-high throughput of systems like the PromethION, GridION strikes a compelling balance.
User-friendly platform: GridION's simplified setup, intuitive interface, and integrated computing power make it an attractive option for researchers who may be new to nanopore sequencing or prefer a streamlined workflow.
Competitive cost: When long reads are essential, but budgets are constrained, the GridION offers a compelling cost-of-ownership model compared to some other long-read sequencing technologies.

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This information on this page is up-to-date as of May 1, 2024 and based on the spec sheets published by the manufacturer.