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

Author

Listed:
  • Ying Chen

    (Sun Yat-sen University)

  • Fan Nie

    (Central South University)

  • Shang-Qian Xie

    (Hainan University
    Hainan University)

  • Ying-Feng Zheng

    (Sun Yat-sen University)

  • Qi Dai

    (Zhejiang Sci-Tech University)

  • Thomas Bray

    (Oxford Nanopore Technologies)

  • Yao-Xin Wang

    (Zhejiang Sci-Tech University)

  • Jian-Feng Xing

    (Hainan University
    Hainan University)

  • Zhi-Jian Huang

    (Sun Yat-sen University
    Sun Yat-sen University
    Sun Yat-sen University)

  • De-Peng Wang

    (Nextomics Biosciences Co., Ltd)

  • Li-Juan He

    (Sun Yat-sen University)

  • Feng Luo

    (Clemson University)

  • Jian-Xin Wang

    (Central South University
    Central South University)

  • Yi-Zhi Liu

    (Sun Yat-sen University
    Chinese Academy of Medical Sciences)

  • Chuan-Le Xiao

    (Sun Yat-sen University)

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.

Suggested Citation

  • Ying Chen & Fan Nie & Shang-Qian Xie & Ying-Feng Zheng & Qi Dai & Thomas Bray & Yao-Xin Wang & Jian-Feng Xing & Zhi-Jian Huang & De-Peng Wang & Li-Juan He & Feng Luo & Jian-Xin Wang & Yi-Zhi Liu & Chu, 2021. "Efficient assembly of nanopore reads via highly accurate and intact error correction," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-020-20236-7
    DOI: 10.1038/s41467-020-20236-7
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    Cited by:

    1. Rubén Barcia-Cruz & David Goudenège & Jorge A. Moura de Sousa & Damien Piel & Martial Marbouty & Eduardo P. C. Rocha & Frédérique Roux, 2024. "Phage-inducible chromosomal minimalist islands (PICMIs), a novel family of small marine satellites of virulent phages," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    2. Yaohua You & H. M. Suraj & Linda Matz & A. Lorena Herrera Valderrama & Paul Ruigrok & Xiaoqian Shi-Kunne & Frank P. J. Pieterse & Anne Oostlander & Henriek G. Beenen & Edgar A. Chavarro-Carrero & Si Q, 2024. "Botrytis cinerea combines four molecular strategies to tolerate membrane-permeating plant compounds and to increase virulence," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Kunpeng Li & Peng Xu & Jinpeng Wang & Xin Yi & Yuannian Jiao, 2023. "Identification of errors in draft genome assemblies at single-nucleotide resolution for quality assessment and improvement," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    4. Ana Paula Zotta Mota & Georgios D. Koutsovoulos & Laetitia Perfus-Barbeoch & Evelin Despot-Slade & Karine Labadie & Jean-Marc Aury & Karine Robbe-Sermesant & Marc Bailly-Bechet & Caroline Belser & Art, 2024. "Unzipped genome assemblies of polyploid root-knot nematodes reveal unusual and clade-specific telomeric repeats," Nature Communications, Nature, vol. 15(1), pages 1-18, December.

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