De novo diploid genome assembly using long noisy reads

Fan Nie, Peng Ni, Neng Huang, Jun Zhang, Zhenyu Wang, Chuanle Xiao (), Feng Luo () and Jianxin Wang ()
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Fan Nie: Central South University
Peng Ni: Central South University
Neng Huang: Central South University
Jun Zhang: 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

Nature Communications, 2024, vol. 15, issue 1, 1-15

Abstract: 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.

Date: 2024
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DOI: 10.1038/s41467-024-47349-7

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