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De novo diploid genome assembly using long noisy reads

Author

Listed:
  • Fan Nie

    (Central South University
    Xiangjiang Laboratory
    Xiangtan University)

  • Peng Ni

    (Central South University
    Xiangjiang Laboratory
    Central South University)

  • Neng Huang

    (Central South University
    Xiangjiang Laboratory
    Central South University)

  • Jun Zhang

    (Central South University
    Xiangjiang Laboratory
    Central South University)

  • Zhenyu Wang

    (Guangdong Academy of Sciences)

  • Chuanle Xiao

    (Sun Yat-sen University #7 Jinsui Road, Tianhe District)

  • Feng Luo

    (Clemson University)

  • Jianxin Wang

    (Central South University
    Xiangjiang Laboratory
    Central South University)

Abstract

The high sequencing error rate has impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, we present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads. We design a haplotype-aware error correction method that can retain heterozygote alleles while correcting sequencing errors. We combine a corrected read SNP caller and a raw read SNP caller to further improve the identification of inconsistent overlaps in the string graph. We use a grouping method to assign reads to different haplotype groups. PECAT efficiently assembles diploid genomes using Nanopore R9, PacBio CLR or Nanopore R10 reads only. PECAT generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads.

Suggested Citation

  • Fan Nie & Peng Ni & Neng Huang & Jun Zhang & Zhenyu Wang & Chuanle Xiao & Feng Luo & Jianxin Wang, 2024. "De novo diploid genome assembly using long noisy reads," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    • Handle: RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-47349-7
    DOI: 10.1038/s41467-024-47349-7
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    References listed on IDEAS

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    1. Erich D. Jarvis & Giulio Formenti & Arang Rhie & Andrea Guarracino & Chentao Yang & Jonathan Wood & Alan Tracey & Francoise Thibaud-Nissen & Mitchell R. Vollger & David Porubsky & Haoyu Cheng & Mobin , 2022. "Semi-automated assembly of high-quality diploid human reference genomes," Nature, Nature, vol. 611(7936), pages 519-531, November.
    2. Ruibang Luo & Fritz J. Sedlazeck & Tak-Wah Lam & Michael C. Schatz, 2019. "A multi-task convolutional deep neural network for variant calling in single molecule sequencing," Nature Communications, Nature, vol. 10(1), pages 1-11, December.
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