De novo diploid genome assembly using long noisy reads

Release time:2025-03-05

DOI number:10.1038/s41467-024-47349-7

Journal:NATURE COMMUNICATIONS

Key Words:SEQUENCE，ALIGNMENT

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 (BisonxSimmental) using Nanopore R9 reads and phase block NG50 with 59.4/58.0 Mb for HG002 using Nanopore R10 reads. Most existing assemblers failed to generate high-quality phased assemblies using long noisy reads. Here, the authors present PECAT, a Phased Error Correction and Assembly Tool, for reconstructing diploid genomes from long noisy reads.

Note:Nie, F (Nie, Fan) [1] , [2] , [3] , [4] ; Ni, P (Ni, Peng) [1] , [2] , [5] ; Huang, N (Huang, Neng) [1] , [2] , [5] ; Zhang, J (Zhang, Jun) [1] , [2] , [5] ; Wang, ZY (Wang, Zhenyu) [6] ; Xiao, CL (Xiao, Chuanle) [7] ; Luo, F (Luo, Feng) [8] ; Wang, JX (Wang, Jianxin) [1] , [2] , [5]

Indexed by:Journal paper

Volume:15

Issue:1

Translation or Not:no

Date of Publication:2024-04-05

Included Journals:SCI