State Key Laboratory of Ophthalmology, Zhongshan Ophthalmic Center, Sun Yat-sen University, #7 Jinsui Road, Tianhe District, Guangzhou, People's Republic of China.
School of Information Science and Engineering, Central South University, Changsha, 410083, People's Republic of China.
Nat Commun. 2021 Jan 4;12(1):60. doi: 10.1038/s41467-020-20236-7.
Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
长纳米孔读长在从头基因组组装中具有优势。然而，纳米孔读通常具有广泛的错误分布和高错误率的序列。现有的错误校正工具不能有效地校正纳米孔读。大多数方法在错误校正过程中修剪高错误率的序列，这减少了读的长度和最终组装的连续性。在这里，我们开发了一种错误校正和从头组装工具，旨在克服纳米孔读中的复杂错误。我们提出了一种自适应读选择和两步渐进方法，以快速将纳米孔读校正到高精度。我们引入了一个两阶段的组装器来利用纳米孔读的全长。我们的工具在纳米孔读的错误校正和从头组装方面都具有优异的性能。它只需要 8122 小时就能组装一个 35X 覆盖的人类基因组，并且在 NG50 上提高了 2.47 倍。此外，我们对人类 WERI 细胞系的组装结果显示 NG50 为 22 Mbp。纳米孔读的高质量组装可以显著减少结构变异检测中的假阳性。
