New Algorithm Enables Near T2T Assembly with Standard ONT Simplex Reads
A newly published study on bioRxiv introduces hifiasm-ONT, a groundbreaking genome assembly algorithm that enables partially phased, near telomere-to-telomere (T2T) assemblies using standard Oxford Nanopore Simplex reads and conventional sample preparation. This advancement significantly broadens access to high-quality genome assemblies without the need for ultra-long reads or complex workflows.
Developed by Haoyu Cheng, Han Qu, Heng Li, and Peter Park—alongside contributions from Oxford Nanopore’s machine learning and applications teams—hifiasm-ONT is a major step forward in genome assembly. It harnesses the power of Nanopore’s Simplex reads, which are generated using standard ligation-based sequencing kits and offer impressive read lengths (typically 30 kb N50), to produce highly contiguous assemblies while lowering data and compute demands.
Unlocking Advanced Genome Assembly—With Simplicity
Traditional telomere-to-telomere genome assembly often requires ultra-long reads or intricate, multi-step protocols. These methods, while powerful, can be expensive and logistically complex, making them inaccessible to many researchers. Hifiasm-ONT offers a practical alternative: by eliminating the need for ultra-long reads and working with commonly available tools and protocols, it opens the door for a broader user base across both research and clinical environments.
“This is a significant moment in the accessibility of near-T2T genome assemblies,” said Gordon Sanghera, CEO of Oxford Nanopore Technologies. “Researchers can now achieve high-quality assemblies using routine Oxford Nanopore workflows, without the need for ultra-long sequencing. In genomics, what you’re missing matters, and this advancement opens the door to information-rich insights across a wider range of applications.”
Performance and Benefits
In testing, hifiasm-ONT outperformed traditional high-accuracy sequencing approaches in several key areas:
- Greater contiguity: The algorithm delivers assemblies with long, uninterrupted sequences that closely approach true telomere-to-telomere spans.
- Lower cost and complexity: By using standard sequencing kits and sample prep methods, users avoid the added expense and labor of specialized protocols.
- Partially phased diploid resolution: Hifiasm-ONT produces assemblies that distinguish between maternal and paternal sequences within contigs, although some haplotype switching still occurs.
- Scalable and accessible: Lower data input and computational demands make this tool suitable for a variety of research settings, including resource-limited labs.
For researchers seeking fully haplotype-resolved assemblies, the algorithm is compatible with the integration of Pore-C or Trio data, which can completely resolve maternal and paternal haplotypes, eliminating phasing ambiguities.
A Leap Forward for Clinical and Biodiversity Genomics
This innovation is particularly relevant for fields like clinical genomics, rare disease research, evolutionary biology, and biodiversity genomics, where understanding complete, accurate genomic structure is critical. The ability to generate near-complete diploid assemblies quickly and cost-effectively makes it easier to study complex genomic regions, including those with high structural variability or previously unresolved sequences.
Hifiasm-ONT also leverages the full potential of Oxford Nanopore’s any-read-length sequencing capabilities. Unlike other platforms that may limit utility based on read length constraints, Oxford Nanopore’s technology can sequence a wide range of fragment sizes, with Simplex reads offering an optimal blend of read length and accuracy for long-range assembly tasks.
Presentation at London Calling 2025
Lead author and algorithm designer Haoyu Cheng will present the details of hifiasm-ONT at London Calling 2025, Oxford Nanopore’s annual genomics conference. His presentation will explore the algorithm’s design, performance benchmarks, and broader implications for the future of scalable, high-quality genome assembly.
About Oxford Nanopore Technologies
Oxford Nanopore Technologies is a global leader in nanopore-based sensing, enabling accessible, real-time molecular analysis. Its platforms are used in over 125 countries to explore the biology of humans, animals, plants, microbes, and entire ecosystems. The company’s goal is to democratize genomic insights—making it possible for anyone, anywhere, to analyze anything.
