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

Chen, Ying, Nie, Fan, Xie, Shang-Qian, Zheng, Ying-Feng, Dai, Qi, Bray, Thomas, Wang, Yao-Xin, Xing, Jian-Feng, Huang, Zhi-Jian, Wang, De-Peng, He, Li-Juan, Luo, Feng, Wang, Jian-Xin, Liu, Yi-Zhi, Xiao, Chuan-Le·2021·Nature Communications
DOI 10.1038/s41467-020-20236-7PMC PMC7782737
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Abstract

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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Research works printed but not linked: 34

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Metadata

Authors
Chen, Y., Nie, F., Xie, S.-Q., Zheng, Y.-F., Dai, Q., Bray, T., Wang, Y.-X., Xing, J.-F., Huang, Z.-J., Wang, D.-P., He, L.-J., Luo, F., Wang, J.-X., Liu, Y.-Z., & Xiao, C.-L.
Venue
Nature Communications
Publisher
Springer Science and Business Media LLC
Published
2021-01-04
Volume
12
Issue
1
ISSN
2041-1723
DOI
10.1038/s41467-020-20236-7
PMC
PMC7782737
Cited by
446
References
1
Language
en
Licence
Funders
  • National Science Foundation (ABI-1759856)
  • United States Department of Agriculture | National Institute of Food and Agriculture (2017-70016-26051)

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