Oxford Nanopore PromethION 2

PromethION 2 is a sequencer released by Oxford Nanopore Technologies in October 2022. It is based on Nanopore Sequencing.

Oxford Nanopore PromethION 2
Image of PromethION 2: https://store.nanoporetech.com/us/p2-solo.html by Oxford Nanopore


Manufacturer Oxford Nanopore Technologies
Technology Nanopore Sequencing
Release date October 2022
Price [2] $100,000
MSRP as of March 2024
Type Benchtop
Weight 13 Kg
Supports real-time analysis Yes
Demultiplexing support Yes
File format FAST5
Read length Oxford Nanopore PromethION 2: Typically 6-20 Kbp
Run time Oxford Nanopore PromethION 2: Up to 72 hours
Reagent cost per Gb [1] Oxford Nanopore PromethION 2: Unavailable
Data quality [3] Oxford Nanopore PromethION 2: > Q20 (99%) for Simplex reads, ~Q30 (99.9%) for Duplex reads
Maximum output per run (Gb)[4] Oxford Nanopore PromethION 2: 580.00
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 PromethION 2

The PromethION 2 is a next-generation sequencing (NGS) platform from Oxford Nanopore Technologies released in 2022 and designed for small to medium-sized academic and research labs, core facilities, and commercial service providers. It fills the gap between the portable MinION and GridION sequencers and the high-throughput PromethION 24/48 systems.

Key Innovations

The PromethION 2's core innovation lies in its modular design and scalability. Unlike its predecessor, the PromethION, which offered a single large instrument configuration, the PromethION 2 comes in two distinct options:

  • PromethION 2 Solo (P2S): This compact and user-friendly benchtop sequencer is ideal for labs with lower throughput requirements. It accommodates two PromethION flow cells, enabling researchers to generate hundreds of gigabases of data per run. The P2 Solo's small footprint makes it easy to integrate into existing lab environments, especially the GridION.
  • PromethION 2 Integrated (P2i): This larger version caters to labs seeking a more integrated solution. The P2i houses two PromethION flow cells alongside built-in high-performance computing power. This eliminates the need for a separate computer for basecalling and data analysis, allowing researchers to perform real-time processing and analysis of their sequencing data. The streamlined and integrated workflow is particularly beneficial for projects requiring continuous data monitoring.

Features and Technologies

  • High-throughput sequencing: Each PromethION flow cell can theoretically generate up to 290 gigabases (Gb) of data.
  • Long-read capability: Nanopore sequencing excels at generating long reads, offering researchers a comprehensive view of complex genomes, transcripts, and other biomolecules.
  • Real-time data analysis: The P2i by itself or the P2S if connected with a GridION Mk1 (or similar computer) can perform basecalling in real-time as data is generated by the flow cells.
  • Flexibility: The PromethION 2 design allows labs to explore their sequencing project needs before scaling up to a PromethION 24 or 48.
  • Data Quality: The PromethION 2 sequencing data boasts base accuracies exceeding Q20 (99%) for Simplex reads and Q30 (99.9%) for Duplex reads.

Intended Uses and Specific Applications

The PromethION 2 offers a wide range of applications within the life sciences. Key areas where it finds particular utility include:

  • De novo genome assembly: The instrument’s long-read capability is ideal for assembling complex genomes of plants, animals, fungi, and microbes, facilitating the identification of structural variants (SVs) and repetitive regions. It's also valuable for scaffolding during hybrid assemblies (combining long and short sequencing reads). Oxford Nanopore offers suitable library kits for this, especially the Ultra-long DNA Sequencing kit.
  • Whole transcriptome analysis: PromethION 2 enables the analysis of entire transcriptomes, including the discovery of novel isoforms, fusion transcripts, and quantification of gene expression. Oxford Nanopore's Direct RNA Sequencing kit is well-suited for this application.
  • Targeted Sequencing: Custom or commercial amplicon-based panels can leverage the long-read capabilities of the PromethION 2 for deep sequencing of targeted genomic regions for the efficient study and discovery of genetic variants. A suitable library prep kit is the Nanopore Ligation Sequencing kit.
  • Microbial genomics and Metagenomics: PromethION 2 delivers the ability to resolve complex microbial communities and study viral genomes. Oxford Nanopore's Rapid Sequencing kit allows for fast turnaround times when characterizing pathogens or investigating outbreaks.
  • Epigenetics: Native DNA passed through a nanopore yields information on base modifications like DNA methylation. PromethION 2 offers direct and sensitive profiling of epigenetic modifications without the need for bisulfite conversion or PCR amplification. Suitable library prep kits include Nanopore’s Ligation Sequencing and Ultra-long DNA Sequencing kits.

Comparison with Competing Instruments

  • Oxford Nanopore GridION: Offers more run flexiblity at similar read lengths and accuracy due to it’s ability to run five independent Flongle or MinION flow cells. However, the max data output per run compared to PromethION 2 is lower.
  • Oxford Nanopore PromethION 24/48: These instruments cater to high-throughput sequencing needs with significantly higher data yield per run at similar accuracy and read lengths but come with a larger footprint and higher cost.
  • PacBio Revio: This competitor from Pacific Biosciences utilizes single-molecule long-read sequencing technology as well. The Revio offers a shorter max run time and higher accuracy but with shorter read lengths on average, a lower max theoretical output, and a significantly higher cost and laboratory footprint.

Special Considerations

Researchers may choose the PromethION 2 over other platforms if their priorities are:

  • Mid- to High-Output: PromethION 2 occupies a middle ground between GridION and PromethION 24/48 in terms of data output.
  • Ultra-long reads: PromethION 2 offers the ability to obtain a high amount of long and ultra-long reads that are useful for specific types of projects.
  • Real-time analysis: Although Nanopore sequencing can have longer run times compared to short-read sequencing technology, the runs can be stopped at any time once the required data has been obtained.
  • Low cost: The PromethION 2 is a cost-effective choice for labs who need long reads considering how much output it can provide, as it has a much lower upfront cost and smaller lab footprint than all the PacBio platforms.
  • Flexibility: The P2S and P2i offer different versions of the PromethION that researchers can choose depending on their lab setup.

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This information on this page is up-to-date as of May 2, 2024 and based on the spec sheets published by the manufacturer.