# Long-read sequencing (PacBio, Oxford Nanopore)

Source: https://onco.cc/technologies/long-read-sequencing/  
OnCo record `long-read-sequencing` (Technology). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

Long-read sequencing (PacBio HiFi, Oxford Nanopore) reads single DNA molecules in stretches of thousands of bases, so rearrangements, repeat expansions, gene fusions and methylation appear in one run where short-read machines miss them. Nanopore can classify a brain tumour during surgery in under an hour; throughput per dollar still trails the largest short-read instruments.

## Summary

PacBio HiFi and Oxford Nanopore reads span kilobases, resolving structural variants, phasing, repeat expansions, and base modifications in one run. In oncology: rapid intraoperative methylation classification of brain tumours (nanopore, under an hour), fusion detection, and complex rearrangement mapping. Cost per genome is approaching short-read levels; accuracy is now clinical-grade for HiFi.

## Fields

- Kind: Technology
- Status: established
- Last checked: 2026-09-08
- Tags: supporting
- Principle: Single-molecule real-time fluorescence (PacBio) or ionic current through a protein nanopore (ONT) reads native or circular-consensus molecules without amplification.
- Strengths: Structural variants and methylation natively; Fast, portable (nanopore)
- Limitations: Higher per-base error historically (improving); Lower throughput per dollar than the largest short-read instruments

## Sources

- Logsdon et al., Long-read human genome sequencing and its applications (Nature Reviews Genetics 2020): https://doi.org/10.1038/s41576-020-0236-x

## Connected records

- fronts: [Diagnostics & Biomarkers](https://onco.cc/fronts/diagnostics/), [Drug Discovery Platforms](https://onco.cc/fronts/drug-discovery/)
- technologies: [DNA methylation profiling](https://onco.cc/technologies/methylation-profiling/), [Whole-exome & whole-genome sequencing](https://onco.cc/technologies/wes-wgs/)
- companies: [Oxford Nanopore Technologies](https://onco.cc/companies/oxford-nanopore/), [PacBio](https://onco.cc/companies/pacbio/)
- key papers: [Long-read human genome sequencing and its applications](https://onco.cc/key-papers/paper-logsdon-nat-rev-genet/)
- roadmaps: [Diagnostics roadmap: stains → gene panels → blood tests that decide treatment](https://onco.cc/roadmaps/diagnostics-roadmap/)

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