de novo diploid genome assembly using long noisy reads via haplotype-aware error correction and inconsistent overlap identification

High sequencing errors have impeded the application of long noisy reads for diploid genome assembly. Most existing assemblers failed to distinguish heterozygotes from high sequencing errors in long noisy reads and generate collapsed assemblies with lots of haplotype switches. 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 develop a read-level SNP caller that can further reduce the SNP errors in corrected reads. Then, we use a read grouping method to assign reads to different haplotype groups. To accelerate the assembling, PECAT only performs local alignment when it is necessary. PECAT efficiently assembles diploid genomes using only long noisy reads and generates more contiguous haplotype-specific contigs compared to other assemblers. Especially, PECAT achieves nearly haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore reads.