TY  - JOUR
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
Y1  - 2024/11/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1919 
EP  - 1930 
DO  - 10.1101/gr.279334.124 
VL  - 34 
IS  - 11 
UR  - http://genome.cshlp.org/content/34/11/1919.abstract 
N2  - 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. 
ER  -