RT Journal
A1 Koren, Sergey
A1 Bao, Zhigui
A1 Guarracino, Andrea
A1 Ou, Shujun
A1 Goodwin, Sara
A1 Jenike, Katharine M.
A1 Lucas, Julian
A1 McNulty, Brandy
A1 Park, Jimin
A1 Rautiainen, Mikko
A1 Rhie, Arang
A1 Roelofs, Dick
A1 Schneiders, Harrie
A1 Vrijenhoek, Ilse
A1 Nijbroek, Koen
A1 Nordesjo, Olle
A1 Nurk, Sergey
A1 Vella, Mike
A1 Lawrence, Katherine R.
A1 Ware, Doreen
A1 Schatz, Michael C.
A1 Garrison, Erik
A1 Huang, Sanwen
A1 McCombie, William Richard
A1 Miga, Karen H.
A1 Wittenberg, Alexander H.J.
A1 Phillippy, Adam M.
T1 Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
JF Genome Research 
JO Genome Research 
YR 2024 
FD November 01 
VO 34 
IS 11 
SP 1919 
OP 1930 
DO 10.1101/gr.279334.124 
UL http://genome.cshlp.org/content/34/11/1919.abstract 
AB The combination of ultra-long (UL) Oxford Nanopore Technologies (ONT) sequencing reads with long, accurate Pacific Bioscience (PacBio) High Fidelity (HiFi) reads has enabled the completion of a human genome and spurred similar efforts to complete the genomes of many other species. However, this approach for complete, “telomere-to-telomere” genome assembly relies on multiple sequencing platforms, limiting its accessibility. ONT “Duplex” sequencing reads, where both strands of the DNA are read to improve quality, promise high per-base accuracy. To evaluate this new data type, we generated ONT Duplex data for three widely studied genomes: human HG002, Solanum lycopersicum Heinz 1706 (tomato), and Zea mays B73 (maize). For the diploid, heterozygous HG002 genome, we also used “Pore-C” chromatin contact mapping to completely phase the haplotypes. We found the accuracy of Duplex data to be similar to HiFi sequencing, but with read lengths tens of kilobases longer, and the Pore-C data to be compatible with existing diploid assembly algorithms. This combination of read length and accuracy enables the construction of a high-quality initial assembly, which can then be further resolved using the UL reads, and finally phased into chromosome-scale haplotypes with Pore-C. The resulting assemblies have a base accuracy exceeding 99.999% (Q50) and near-perfect continuity, with most chromosomes assembled as single contigs. We conclude that ONT sequencing is a viable alternative to HiFi sequencing for de novo genome assembly, and provides a multirun single-instrument solution for the reconstruction of complete genomes.