Long-read sequencing services

01Overview and value chain

Markers: [EC: IVDR 2017/746 (EU) + FDA LDT/IVD oversight + ISO 15189 | OECD: Genomics & bioinformatics | Regulator: FDA (USA), NMPA (China)]

Long-read (third-generation) sequencing reads DNA fragments of 10,000 to over one million bases continuously, where Illumina short-read NGS reads only about 150-300 bases. Those long reads resolve highly repetitive regions (centromeres, telomeres, segmental duplications), close the gaps short reads leave in reference genomes, and enable telomere-to-telomere de novo assembly. Two platform duopolists dominate: Oxford Nanopore (ONT), which passes a single DNA or RNA strand through a protein nanopore and reads the ionic-current changes, allowing direct sequencing of native DNA and RNA with simultaneous 5mC / 5hmC / m6A methylation detection and no PCR amplification; and PacBio SMRT, whose Zero-Mode Waveguides perform circular-consensus sequencing to produce HiFi reads roughly 15-20 kb long at greater than 99.9% accuracy (Q30). Services span de novo assembly, structural-variant detection, haplotype phasing, metagenomics and clinical genetics, regulated as IVD / LDT by the FDA and NMPA and under the EU IVDR. The six organizations in this projection span the two platforms (Oxford Nanopore, PacBio) and the service ecosystem (NextOmics, Genoscope, Broad Institute, SciLifeLab).

Key directions of long-read sequencing services:

1. Telomere-to-telomere de novo assembly: long reads close repeats and gaps that short reads cannot resolve.
2. Direct epigenetic detection: native 5mC / 5hmC / m6A without bisulfite conversion (ONT) or from polymerase kinetics (PacBio).
3. Structural-variant and clinical genetics: balanced translocations and repeat-expansion disorders undetectable by short reads.
4. Field and environmental metagenomics: portable MinION real-time ocean and soil surveillance (Genoscope).

Sectoral value chain

[HMW DNA extraction] ──> [library prep] ──> [sequencing run] ──> [basecalling]
                                                                  │
                                                    (epigenetics + assembly)
                                                                  │
                                                                  ▼
[validated report] <─── [bioinformatics] <─────┘

Value chain levels

Cross-cutting technologies of the sector:

• nanopore-sequencing: direct-strand DNA/RNA through protein nanopores with AI basecalling (Dorado).
• smrt-sequencing: circular-consensus HiFi reads in Zero-Mode Waveguides (PacBio Revio).
• genome-assembly: OLC assemblers (Flye, Hifiasm, Minimap2) for de novo assembly and phasing.

02US

The United States leads high-accuracy long-read sequencing through the PacBio platform monopoly and the largest federal academic sequencing cores.

PacBio platforms, pangenome reference, FDA oversight

• PacBio: the Revio, Onso and Vega long-read systems; its new SPRQ-Nx chemistry, shipping in 2026, brings HiFi whole-human genomes below USD 300 each, enabling large cohort projects.
• Broad Institute: develops pangenome and de novo assembly pipelines and contributes to the Human Pangenome Reference Consortium (HPRC), replacing the flat GRCh38 reference with a graph that captures population diversity.
• NIH All of Us long-read core: integrates PacBio Revio capacity for structural-variant discovery linked to rare disease.
• FDA LDT / IVD oversight: the regulatory framework under which clinical long-read tests are validated.

03CN

China integrates long-read sequencing into clinical genetics and oncology and operates the largest dedicated long-read service factory in the region.

long-read CRO, co-barcoding, clinical structural variants

• NextOmics (Wuhan): operates one of Asia’s largest long-read factories, running dozens of PacBio Revio and ONT PromethION systems for plant, animal and human de novo genome services.
• BGI stLFR: single-tube long-fragment-read co-barcoding that emulates long reads from inexpensive short reads on MGI instruments.
• Clinical SV screening: prenatal and oncology centres pioneer routine long-read detection of balanced translocations and repeat-expansion disorders, under NMPA IVD oversight.

04EU

The European Union leads portable and environmental nanopore sequencing, anchored by Oxford Nanopore and a dense network of national bioinformatics institutes.

Oxford Nanopore, environmental metagenomics, clinical genomics

• Oxford Nanopore (Oxford): the MinION portable sequencer and the high-throughput PromethION 48, plus the PromethION 2 Solo that puts cheap long reads in reach of small labs; R10.4.1 chemistry with direct DNA/RNA and methylation reading.
• Genoscope (France): the national sequencing centre uses nanopores for real-time ocean and soil metagenomic surveillance (e.g. nanoMDBG metagenome assembly).
• SciLifeLab (Sweden): a national infrastructure whose Clinical Genomics unit delivers long-read diagnostics, contributing to the European Pangenome Consortium.

05Leading companies and research institutes

06Tech stack and innovations

The stack combines protein-engine nanopores, nanofabricated optical chips and specialized long-read assembly algorithms.

1. Nanopore sequencing (ONT):
   • an engineered protein channel (R10.4.1, a CsgG mutant) sits in a synthetic membrane; a motor helicase ratchets single-stranded DNA through at roughly 400 bases per second, and the ionic-current trace is decoded into bases by a deep-learning basecaller (Dorado), reading native DNA, RNA and methylation directly.
2. SMRT circular-consensus sequencing (PacBio):
   • Zero-Mode Waveguides (~100 nm wells) each immobilize a single polymerase; a circular SMRTbell template is read repeatedly and consensus-collapsed into HiFi reads at Q30 (>99.9%), and the new SPRQ-Nx chemistry drives HiFi human genomes below USD 300.
3. Assembly bioinformatics:
   • because long reads defeat de-Bruijn short-read assemblers, OLC assemblers take over — Flye for nanopore and Hifiasm for diploid/polyploid HiFi phasing — with Minimap2 for alignment, producing telomere-to-telomere assemblies.

07Value chains and production pipelines

Industrial pipeline of a de novo pathogen-genome assembly on PacBio Revio (ISO 15189)

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. HMW DNA extraction     │ ───> │ 2. SMRTbell library       │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. ZMW sequencing (Revio) │ <─── │ 3. SMRT cell loading      │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. CCS basecall + 5mC     │ ───> │ 6. Hifiasm assembly       │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: HMW DNA extraction

High-molecular-weight DNA is gently isolated (avoiding shearing) from the pathogen culture and quality-checked for fragment length, concentration and purity.

Stage 2: SMRTbell library preparation

The HMW DNA is sized and ligated with hairpin adapters to form closed circular SMRTbell templates, then cleaned of unligated material.

Stage 3: SMRT cell loading

Polymerase is bound to the primed SMRTbell templates and the complexes are loaded onto a Revio SMRT cell, settling into the Zero-Mode Waveguide wells.

Stage 4: ZMW sequencing

The Revio images the wells in real time as fluorescent nucleotides are incorporated, recording the circular reads over a 24-hour run.

Stage 5: CCS basecalling and modification calling

On-board GPUs collapse the repeated reads into high-accuracy HiFi consensus sequences and call 5mC methylation from inter-pulse kinetics.

Stage 6: Hifiasm assembly

Hifiasm performs a de novo telomere-to-telomere assembly from the HiFi reads, overlays the methylation map, and a LIMS report is filed for clinical or surveillance use.