Oxford Nanopore Sequencing: Devices, Flow Cells and How It Works

This page is for researchers and core-facility staff who need to understand what Oxford Nanopore Technologies (ONT) sequencing is, how the signal becomes a sequence, and how the MinION, GridION and PromethION device tiers differ. After reading it you should be able to place the platform next to other sequencing approaches and know which output files to expect. Facts are taken from the manufacturer’s technology page and from the public-education resource Your Genome, both read on 2026-11-07.

What is nanopore sequencing?

Nanopore sequencing reads DNA or RNA by passing a single molecule through a nanoscale protein channel and recording how the electric current changes as it moves. Oxford Nanopore Technologies is the company that commercialises this approach, and its instruments are often described as third-generation sequencers because they do not use a DNA polymerase to copy the template while reading it (Your Genome, 2026-11-07).

Because the molecule itself is measured, no amplification step is needed: native DNA or RNA is analysed and base modifications such as methylation stay present in the signal (Oxford Nanopore technology page, 2026-11-07). Read length is set by the length of the input molecule rather than by the chemistry; the manufacturer cites reads from 20 to 4,000,000 bases.

How does nanopore sequencing work?

In short: a motor protein feeds a molecule through a pore, a voltage drives it, and software turns the resulting current trace into bases. The stages, as the manufacturer describes them:

1. Library preparation. Sequencing adapters carrying a preloaded motor protein are attached to the sample. The manufacturer states preparation can take as little as 10 minutes.
2. Loading a flow cell. Thousands of engineered protein nanopores sit in an electrically resistant membrane inside the flow cell.
3. Translocation. The motor protein binds the pore and sets the speed of travel. For double-stranded DNA it separates the strands first; RNA is read directly as a single strand.
4. Current measurement. An applied voltage pulls the molecule through the pore. Each combination of bases in the pore produces a characteristic change in ionic current.
5. Basecalling. Algorithms translate the signal into sequence. Basecalling runs in the MinKNOW software, which also powers Adaptive Sampling, ONT’s on-device targeted enrichment.

Your Genome describes the pore as a barrel-shaped protein (alpha-hemolysin) roughly 1 nm wide held in an artificial membrane, with a chip that measures the disruption in current.

How does nanopore seq work, in one sentence?

A voltage pulls a DNA or RNA strand through a protein pore, the current signature of the bases inside the pore is recorded, and basecalling software converts that signature to sequence.

Oxford Nanopore devices: MinION, GridION and PromethION

The manufacturer’s technology page lists four device formats, which differ in how many flow cells they run rather than in the underlying principle:

Device	Format	Flow cells (per manufacturer)
MinION	Portable	One flow cell
GridION	Benchtop	Up to five independent MinION flow cells
PromethION 2 Integrated	Integrated device	Up to two high-output PromethION flow cells
PromethION 24	Large-scale	Up to 24 PromethION flow cells

A flow cell is the consumable that holds the nanopores. Your Genome notes that the smallest devices are roughly phone- to microwave-sized and need only a laptop; the smallest has been used on the International Space Station.

What data does a nanopore run produce?

The raw measurement is the electrical signal. Basecalling converts it to reads, which analysis pipelines typically handle as FASTQ files with per-base quality scores. For how those files are laid out, see our guides to the FASTQ format and Phred quality scores. Downstream steps such as de novo genome assembly take those reads as input. Because modifications such as methylation are visible in the signal, they can be read without a separate conversion step (manufacturer technology page).

Strengths and limits

Aspect	What the sources state
Read length	Determined by input molecule length; manufacturer cites 20 to 4,000,000 bases. Your Genome: ultra-long reads of up to several million base pairs.
Sample handling	No amplification; native DNA and RNA are read; base modifications retained.
Portability	MinION is portable; devices need only a laptop (Your Genome).
Speed in the field	Your Genome reports genomes from 14 patients within 48 hours during the 2015 Ebola outbreak.
Accuracy	Your Genome states the technology has lower accuracy than other technologies.

Alternatives and how they differ

Approach	Key difference from nanopore	Read more
Oxford Nanopore	Measures current through a protein pore; no polymerase or amplification step	This page
Illumina sequencing-by-synthesis	Reads by synthesis rather than pore measurement	Illumina (Solexa) sequencing, Illumina vs Nanopore
PacBio	A separate sequencing platform	PacBio DNA sequencing

For the broader field, see DNA sequencing.

FAQ

What is nanopore sequencing?

A method that identifies the bases of a single DNA or RNA molecule from the current changes it causes while passing through a protein nanopore, without amplification (manufacturer technology page, 2026-11-07).

Can you sequence a genome at home?

The devices are small and, per Your Genome, need only a laptop, so the instrument itself is not a barrier. The work still involves library preparation, flow-cell loading and bioinformatics, so it is a laboratory method rather than a consumer test. This page does not give procedural or medical guidance; follow the manufacturer’s documentation and your institution’s safety and ethics rules.

What are the advantages of genomic sequencing?

Sequencing lets researchers read the genetic makeup of organisms to study function, variation and disease; see what genomics is for the field overview. For nanopore specifically, the sourced advantages are long reads, no amplification and retained base modifications.

What is the difference between MinION and PromethION?

MinION is the portable single-flow-cell device. PromethION systems run high-output PromethION flow cells, up to 2 on the PromethION 2 Integrated and up to 24 on the PromethION 24.

Sources

• Oxford Nanopore Technologies, platform technology page, nanoporetech.com/platform/technology, read 2026-11-07.
• Your Genome (Wellcome Connecting Science), “What is Oxford Nanopore Technology (ONT) sequencing?”, yourgenome.org, read 2026-11-07.