Nanopore direct RNA sequencing

01Overview and value chain#

Markers EC: RUO boundary for native-RNA transcriptomics; IVD edge marked by GridION Dx CE-IVD/UKCA | OECD: Genomics & bioinformatics | Regulator: FDA (USA), EMA (EU)

Direct RNA sequencing reads an RNA molecule the way it exists in the cell: the native strand passes through a protein nanopore, each base disturbs an ionic current, and the current trace is decoded into sequence. Because the molecule is never reverse-transcribed into cDNA and never amplified, the two distortions that shape most transcriptomics disappear — reverse-transcription bias, which under- and over-represents transcripts, and PCR amplification, which erases the chemical record. That chemical record is the platform’s distinctive output: base modifications such as m6A leave characteristic current signatures, so modification mapping runs on the same read that gives the sequence, not on a separate chemistry. The corpus’s ledger evidence pairs a chemistry owner with a deployment. Oxford Nanopore owns the platform end: the UK-listed sequencing company (LSE: ONT) runs production at the Harwell Campus in Didcot and the Spectrum facility in Abingdon, builds more than a million flow cells a year, manufactures under ISO 13485, and marks its GridION Dx configuration CE-IVD and UKCA — the regulated edge of a research-first chemistry. Genoscope owns a deployment end: the French national sequencing centre runs nanopores for real-time surveillance of ocean and soil metagenomes, with the nanoMDBG metagenome assembly as its published instrument and the €41.3 million ATLASea program (2024) as its marine-genome mandate. The boundary against sibling pages: long-read-sequencing-services owns the service layer and the PromethION DNA long-read row; spatial-transcriptomics owns measurement geometry; bioinformatics-multi-omics owns the downstream analysis. This page owns the native-RNA chemistry itself.

Key directions of nanopore direct RNA sequencing:

1. Native-RNA chemistry (No Conversion): the strand is read as RNA, so reverse-transcription bias and amplification distortion never enter the measurement.
2. Modification-aware reads (Chemistry as Signal): m6A-class base modifications appear in the raw ionic current, making modification mapping a property of the read rather than a separate assay.
3. Real-time environmental surveillance (Nanopores in the Field): Genoscope’s ocean and soil metagenome monitoring, assembled through nanoMDBG, runs sequencing as a live instrument rather than a batch service.
4. Isoform-resolved transcriptomics (Full-Length Reads): full-length strand reads resolve isoforms directly, with barcode-aware adaptive sampling and an updated cDNA-PCR kit extending the platform’s transcriptomic reach.

Sectoral value chain#

[native RNA sample] ──> [direct-RNA library prep] ──> [pore flow cell]
                                                            │
                                                (live basecalling, modifications)
                                                            ▼
[surveillance / transcriptomics] <── [real-time analysis] <── [current-trace reads]

Value chain levels#

Cross-cutting technologies of the sector:

• Adaptive sampling (Selective Reading): the platform rejects or retains molecules mid-read, steering capacity toward targets of interest.
• Metagenome assembly pipelines (Field-Grade Assembly): nanoMDBG-class assemblers turn noisy metagenomic reads into usable genomes in surveillance settings.
• Diagnostic device compliance (The IVD Edge): CE-IVD and UKCA marking on the GridION Dx configuration separates the research chemistry from the regulated diagnostic device.

02US#

The direct-RNA ledger record has no US rows yet, so this section records the structural frame rather than vendor claims.

Research-use chemistry, the IVD boundary, no US ledger rows#

• RUO framing: native-RNA transcriptomics runs as research-use chemistry; the FDA research/diagnostic boundary is what a clinical claim would have to cross.
• Ledger gap: no sourced US direct-RNA deployment dossiers exist yet — a screen-wave target.
• Ownership note: the platform company is UK-listed (LSE: ONT); US market presence is not carried in the ledger evidence.

03CN#

China appears in the ledger evidence as equipment inside a European deployment, not as a direct-RNA ledger row.

CN platforms in the platform mix, no direct-RNA ledger depth#

• MGI DNBSEQ-G400 in the mix: Genoscope’s sequencer fleet pairs Oxford Nanopore pores with Illumina and MGI short-read platforms — a CN-made platform inside the ledgered deployment.
• Ledger gap: no sourced CN direct-RNA dossiers exist yet — a screen-wave target.

04EU#

Europe carries both ends of the ledgered value chain: the UK chemistry owner and the French national deployment.

UK production, French surveillance, regulated edge#

• Oxford Nanopore (Oxford, UK): 1,314 employees; production at the Harwell Campus (Didcot) and the Spectrum facility (Abingdon); more than one million flow cells per year; ISO 13485 manufacturing; GridION Dx marked CE-IVD and UKCA.
• Genoscope (Evry-Courcouronnes, France): the national sequencing centre at the Genopole biocluster; real-time ocean and soil metagenome surveillance on MinION, GridION and PromethION pores; nanoMDBG assembly; €41.3 million ATLASea grant (2024) under CEA, France Génomique and ANR funding; a 1,700-core cluster with 1.5 PB storage.

05Leading companies and research institutes#

06Tech stack and innovations#

The stack runs from one intact RNA sample to one deployed insight — and every stage exists to keep the molecule native.

1. Native chemistry (Read What Exists):
   • the strand is never copied, so the sequence and its modifications arrive in one measurement.
   • case: Oxford Nanopore’s direct-RNA and extended transcriptomic kits on MinION, GridION and PromethION hardware.
2. Current-level decoding (Signal as Truth):
   • base modifications are read from the ionic-current trace itself, not inferred from a converted copy.
   • case: modification-aware basecalling on the platform’s live readout.
3. Surveillance-grade analysis (Sequencing as Instrument):
   • assembly pipelines sized for field conditions turn streams of reads into monitoring output.
   • case: Genoscope’s nanoMDBG metagenome assembly behind its ocean and soil programs.

07Value chains and production pipelines#

Industrial pipeline of a direct-RNA sequencing campaign (native-molecule regime)#

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Sample to native RNA   │ ───> │ 2. Library preparation    │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. Live basecalling       │ <─── │ 3. Pore flow cell         │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Real-time analysis     │ ───> │ 6. Deployed insight       │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Sample to native RNA

Intact, full-length RNA is recovered from the biological sample without amplification.

Stage 2: Library preparation

Adapters are ligated to native strands; an updated cDNA-PCR kit extends the route where RNA input is limited.

Stage 3: Pore flow cell

The library loads onto a flow cell; strands translocate through protein pores one molecule at a time. Production capacity exceeds one million flow cells per year at the Harwell plant.

Stage 4: Live basecalling

Ionic-current traces decode into sequence and modification calls as the read passes — barcode-aware adaptive sampling steers the run mid-flight.

Stage 5: Real-time analysis

Assembly and surveillance pipelines process reads while the run continues; nanoMDBG-class assembly supports environmental monitoring.

Stage 6: Deployed insight

Transcriptomes, modification maps and surveillance signals become operational output — research findings or environmental alerts.