March 19, 2024 | Sergey Koren, Zhigui Bao, Andrea Guarracino, Shujun Ou, Sara Goodwin, Katharine M. Jenike, Julian Lucas, Brandy McNulty, Jimin Park, Mikko Rautiainen, Arang Rhee, Dick Roelofs, Harrie Schneiders, Ilse Vrijenhoek, Koen Nijbroek, Doreen Ware, Michael C. Schatz, Erik Garrison, Sanwen Huang, W. Richard McCombie, Karen H. Miga, Alexander H.J. Wittenberg, Adam M. Phillippy
The study demonstrates the feasibility of using Oxford Nanopore Technologies (ONT) sequencing to assemble complete human and plant genomes, achieving telomere-to-telomere (T2T) assemblies. The researchers generated ONT Duplex data for the human genome HG002, tomato (*Solanum lycopersicum* Heinz 1706), and maize (*Zea mays* B73). Duplex sequencing, which reads both strands of DNA to improve accuracy, showed similar accuracy to PacBio HiFi sequencing but with longer read lengths. The ONT Duplex data was combined with ultra-long Simplex data and trio data to assemble the genomes. The resulting assemblies had high continuity, with most chromosomes assembled as single contigs, and base accuracy exceeding 99.999%. The study also validated the resolution of centromeric arrays and identified unresolved regions in the tomato and maize genomes. The authors conclude that ONT sequencing is a viable alternative to HiFi sequencing for *de novo* genome assembly, offering a single-instrument solution for the reconstruction of complete genomes.The study demonstrates the feasibility of using Oxford Nanopore Technologies (ONT) sequencing to assemble complete human and plant genomes, achieving telomere-to-telomere (T2T) assemblies. The researchers generated ONT Duplex data for the human genome HG002, tomato (*Solanum lycopersicum* Heinz 1706), and maize (*Zea mays* B73). Duplex sequencing, which reads both strands of DNA to improve accuracy, showed similar accuracy to PacBio HiFi sequencing but with longer read lengths. The ONT Duplex data was combined with ultra-long Simplex data and trio data to assemble the genomes. The resulting assemblies had high continuity, with most chromosomes assembled as single contigs, and base accuracy exceeding 99.999%. The study also validated the resolution of centromeric arrays and identified unresolved regions in the tomato and maize genomes. The authors conclude that ONT sequencing is a viable alternative to HiFi sequencing for *de novo* genome assembly, offering a single-instrument solution for the reconstruction of complete genomes.