Efficient assembly of nanopore reads via highly accurate and intact error correction

By Ying Chen, Fan Nie, Shang-Qian Xie, Yingfeng Zheng, Qi Dai, Thomas Bray, Yaoxin Wang, Jian-feng Xing, Zhiyong Huang, De-Peng Wang and 5 more. Nature Communications, 2021

377 citations recorded by the source corpus.

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. 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.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/c2ed1ebd2881271afa705d74299e2c14843d907b

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In Molecular Biology

1. Zongyi Sun
2. Jiang Hu

Citations in the corpus

• NextDenovo: an efficient error correction and accurate assembly tool for noisy long reads (2024, methodology): “However, in terms of the assembly of segmental duplications/repeats, and especially for large plant genome assemblies, the CTA-based strategy usually has an enhanced ability to distinguish different gene copies and produce more accurate and continuous assemblies [14, 15, 18].”