March 19, 2024 | Sergey Koren, Zhigui Bao, Andrea Guaraccino, Shujun Ou, Sara Goodwin, Katharine M. Jenike, Julian Lucas, Brandy McNulty, Jimin Park, Mikkko Rautiainen, Arang Rhie, 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
This study presents a method for assembling complete human and plant chromosomes using only nanopore sequencing. The approach combines ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads, enabling the completion of a human genome and similar efforts for other species. However, this method relies on multiple sequencing platforms, limiting its accessibility. The study evaluates ONT "Duplex" sequencing, which reads both strands of DNA to improve accuracy, and finds that it is as accurate as HiFi sequencing but with longer read lengths. The study also uses Pore-C chromatin contact mapping to phase haplotypes in diploid genomes. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. The study concludes that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly and has the potential to provide a single-instrument solution for the reconstruction of complete genomes. The study also demonstrates the utility of Duplex sequencing for agricultural genomes, such as tomato and maize, achieving high continuity and resolving most chromosomes as T2T contigs. The study highlights the potential of ONT sequencing for genome assembly, particularly with the recently released Oxford Nanopore "P2" instrument, which offers a cost-effective solution for high-throughput sequencing. The study also addresses challenges in genome assembly, such as resolving complex repeats and rDNA arrays, and shows that ONT sequencing can overcome these challenges. The study provides a detailed methodology for sequencing and assembly, including library preparation, base-calling, and assembly using Verkko. The study also validates the assemblies against existing references and identifies potential issues in the assemblies. Overall, the study demonstrates the potential of ONT sequencing for genome assembly, particularly for human and plant genomes, and highlights the benefits of using a single sequencing platform for this purpose.This study presents a method for assembling complete human and plant chromosomes using only nanopore sequencing. The approach combines ultra-long Oxford Nanopore (ONT) sequencing reads with long, accurate PacBio HiFi reads, enabling the completion of a human genome and similar efforts for other species. However, this method relies on multiple sequencing platforms, limiting its accessibility. The study evaluates ONT "Duplex" sequencing, which reads both strands of DNA to improve accuracy, and finds that it is as accurate as HiFi sequencing but with longer read lengths. The study also uses Pore-C chromatin contact mapping to phase haplotypes in diploid genomes. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. The study concludes that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly and has the potential to provide a single-instrument solution for the reconstruction of complete genomes. The study also demonstrates the utility of Duplex sequencing for agricultural genomes, such as tomato and maize, achieving high continuity and resolving most chromosomes as T2T contigs. The study highlights the potential of ONT sequencing for genome assembly, particularly with the recently released Oxford Nanopore "P2" instrument, which offers a cost-effective solution for high-throughput sequencing. The study also addresses challenges in genome assembly, such as resolving complex repeats and rDNA arrays, and shows that ONT sequencing can overcome these challenges. The study provides a detailed methodology for sequencing and assembly, including library preparation, base-calling, and assembly using Verkko. The study also validates the assemblies against existing references and identifies potential issues in the assemblies. Overall, the study demonstrates the potential of ONT sequencing for genome assembly, particularly for human and plant genomes, and highlights the benefits of using a single sequencing platform for this purpose.