PECAT

PECAT performs haplotype-aware error correction and phased assembly of diploid genomes from long noisy reads to retain heterozygous alleles and produce haplotype-specific contigs.

Key Features:

• Haplotype-aware error correction: Applies a haplotype-aware error correction method that preserves heterozygote alleles while correcting sequencing errors.
• Corrected-read and raw-read SNP callers: Utilizes both a corrected-read SNP caller and a raw-read SNP caller to enhance variant detection.
• Inconsistent-overlap identification: Uses SNP information to identify inconsistent overlaps within the string graph structure.
• Read grouping by haplotype: Groups reads into distinct haplotype groups to guide haplotype-specific assembly.
• Haplotype-specific contig generation: Produces haplotype-specific contigs with improved contiguity and specificity.
• Long-read technology support: Supports Nanopore R9, Nanopore R10, and PacBio CLR long-read sequencing technologies.
• Comparative performance: Generates more contiguous haplotype-specific contigs compared to other assemblers.
• Empirical results — B. taurus: Nearly achieved haplotype-resolved assembly on B. taurus (Bison×Simmental) using Nanopore R9 reads.
• Empirical results — human HG002: Achieved phase block NG50 metrics of 59.4/58.0 Mb for human sample HG002 using Nanopore R10 reads.

Scientific Applications:

• Diploid genome assembly: Construction of phased diploid genome assemblies from long noisy reads.
• Haplotype-resolved assembly and phasing: Generation and evaluation of haplotype-specific contigs and phase block metrics (e.g., NG50).
• Complex eukaryotic genome assembly: Assembly of complex diploid genomes such as B. taurus (Bison×Simmental) using Nanopore or PacBio long reads.

Methodology:

Implements haplotype-aware error correction, applies corrected-read and raw-read SNP callers, identifies inconsistent overlaps in a string graph using SNP information, groups reads by haplotype, and assembles haplotype-specific contigs.