Gapless assembly of complete human and plant chromosomes using only nanopore sequencing

文献类型： 外文期刊

第一作者： Koren, Sergey

作者： Koren, Sergey;Rautiainen, Mikko;Rhie, Arang;Phillippy, Adam M.;Bao, Zhigui;Bao, Zhigui;Huang, Sanwen;Guarracino, Andrea;Garrison, Erik;Ou, Shujun;Goodwin, Sara;Ware, Doreen;Mccombie, William Richard;Jenike, Katharine M.;Schatz, Michael C.;Lucas, Julian;Mcnulty, Brandy;Park, Jimin;Miga, Karen H.;Roelofs, Dick;Schneiders, Harrie;Vrijenhoek, Ilse;Nijbroek, Koen;Wittenberg, Alexander H. J.;Nordesjo, Olle;Nurk, Sergey;Vella, Mike;Lawrence, Katherine R.;Ware, Doreen;Huang, Sanwen

作者机构：

期刊名称：GENOME RESEARCH （ 影响因子：5.5； 五年影响因子：7.3 ）

ISSN： 1088-9051

年卷期： 2024 年 34 卷 11 期

页码：

收录情况： SCI

摘要： 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.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序