Efficient near telomere-to-telomere assembly of nanopore simplex reads
Cheng and Qu et al. introduce hifiasm (ONT), the first algorithm to achieve near telomere-to-telomere (T2T) genome assemblies using standard Oxford Nanopore reads obtained with the Ligation Sequencing Kit — no ultra-long reads required. Providing greater contiguity at a lower cost and computational demand, this algorithm outperforms traditional methods and could make high-quality assemblies accessible for a broad range of applications, from clinical research to biodiversity genomics.
Key points:
Hifiasm (ONT) performs efficient error correction by using phasing information to distinguish true variants from errors
The algorithm assembled highly accurate and contiguous genomes across multiple human and non-human samples
Compared with PacBio HiFi assemblies, Oxford Nanopore assemblies exhibited substantially higher contiguity and comparable quality, even within repetitive regions
Hifiasm (ONT) outperformed Verkko+HERRO in T2T count and contiguity while running an order of magnitude faster and requiring less computational resource
It demonstrated the ability to resolve complex, medically relevant loci such as the highly homologous SMN1 and SMN2 genes that are linked to spinal muscular atrophy
Hifiasm (ONT) enables cost-effective, scalable genome assembly without the need for complex laboratory protocols or high computational overhead
Read our news summary or catch the talk by lead algorithm designer Haoyu Cheng at London Calling 2025 to find out more
Sample type: GIAB data and human cell lines