Chromosome-level haplotype-resolved assembly of highly heterozygous grass genomes with PhaseGrass.

ABSTRACT: Current methods to generate haplotype-resolved assemblies for highly heterozygous genomes suffer from reference bias when relying on reference-based phasing or may generate imbalanced haplomes when relying on graph-based phasing. Here, we report PhaseGrass, an assembly, phasing and scaffolding workflow that is compatible with accurate or error-prone long reads, generating haplotype-resolved assemblies for highly heterozygous genomes. Requiring no parental data, PhaseGrass combines reference-based phasing with haplotype-specific k-mers to partition long reads or unitigs to corresponding haplotypes, thereby avoiding reference bias and uneven haplotype partitioning. Using PhaseGrass, we generated chromosome-level, haplotype-resolved assemblies for the highly heterozygous, allogamous grass spe

SUBMITTER: Chen Y 

PROVIDER: S-EPMC12764793 | biostudies-literature | 2025 Dec

REPOSITORIES: biostudies-literature