Efficient assembly of nanopore reads via highly accurate and intact error correction
发布时间：2025-03-05
点击次数：
DOI码：10.1038/s41467-020-20236-7
发表刊物：NATURE COMMUNICATIONS
关键字：GENOME，ALIGNMENT
摘要：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 8122hours 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. Nanopore reads have been advantageous for de novo genome assembly; however these reads have high error rates. Here, the authors develop an error correction and de novo assembly tool, NECAT, which produces efficient, high quality assemblies of nanopore reads.
备注：Chen, Y (Chen, Ying) [1] ; Nie, F (Nie, Fan) [2] ; Xie, SQ (Xie, Shang-Qian) [3] , [4] ; Zheng, YF (Zheng, Ying-Feng) [1] ; Dai, Q (Dai, Qi) [5] ; Bray, T (Bray, Thomas) [6] ; Wang, YX (Wang, Yao-Xin) [5] ; Xing, JF (Xing, Jian-Feng) [3] , [4] ; Huang, ZJ (Huang, Zhi-Jian) [7] , [8] , [9] ; Wang, DP (Wang, De-Peng) [10] ; He, LJ (He, Li-Juan) [1] ; Luo, F (Luo, Feng) [11] ; Wang, JX (Wang, Jian-Xin) [2] , [12] ; Liu, YZ (Liu, Yi-Zhi) [1] , [13] , [14] ; Xiao, CAL (Xiao, Chuan-Le) [1]
论文类型：期刊论文
卷号：12
期号：1
是否译文：否
发表时间：2021-01-04
收录刊物：SCI