Efficient assembly of nanopore reads via highly accurate and intact error correction.
Efficient assembly of nanopore reads via highly accurate and intact error correction.
复制标题
通过高精度和完整的纠错，高效组装纳米孔读数。
DOI：
10.1038/s41467-020-20236-7
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发表时间：
2021-01-04
影响因子：
16.6
通讯作者：
Xiao CL
中科院分区：
文献类型：
--
作者：
Chen Y;Nie F;Xie SQ;Zheng YF;Dai Q;Bray T;Wang YX;Xing JF;Huang ZJ;Wang DP;He LJ;Luo F;Wang JX;Liu YZ;Xiao CL
长纳米孔读取在从头基因组组装中是有利的。然而，纳米孔读取通常具有宽的错误分布和高错误率的连续性。现有的错误校正工具不能高效且有效地校正纳米孔读数。大多数方法在纠错过程中修剪高错误率的序列，这减少了读段的长度和最终组装的邻接性。在这里，我们开发了一种纠错和从头组装工具，旨在克服纳米孔读取中的复杂错误。我们提出了一种自适应读取选择和两步渐进方法，以快速校正纳米孔读取到高精度。我们引入了两阶段组装器来利用纳米孔读取的全长。我们的工具在错误校正和从头组装纳米孔读取方面都实现了上级性能。仅需8122小时即可组装35倍覆盖率的人类基因组，NG50提高了2.47倍。此外，我们组装的人WERI细胞系显示出22 Mbp的NG50。纳米孔读数的高质量组装可以显著减少结构变异检测中的假阳性。
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.
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影响因子：
46.9
作者：
Jain M;Olsen HE;Turner DJ;Stoddart D;Bulazel KV;Paten B;Haussler D;Willard HF;Akeson M;Miga KH
通讯作者：
Miga KH
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
12.3
作者：
Rang FJ;Kloosterman WP;de Ridder J
通讯作者：
de Ridder J
影响因子：
16.6
作者：
Michael TP;Jupe F;Bemm F;Motley ST;Sandoval JP;Lanz C;Loudet O;Weigel D;Ecker JR
通讯作者：
Ecker JR
影响因子：
48
作者：
Sedlazeck FJ;Rescheneder P;Smolka M;Fang H;Nattestad M;von Haeseler A;Schatz MC
通讯作者：
Schatz MC