HaploSync

HaploSync assembles draft diploid genome sequences into chromosome-scale fully phased pseudomolecules by scaffolding guided by genetic maps and genomes of closely related species for accurate diploid genome reconstruction.

Key Features:

• Phased Pseudomolecule Construction: Scaffolds sequences from a draft diploid genome assembly using genetic maps and/or genomes of closely related species to produce fully phased pseudomolecules.
• Quality Control and Visualization: Implements quality control measures and generates reports visualizing relationships between current and legacy sequences for both haplotypes, including gene and marker content to identify misassemblies.
• Error Correction and Gap Filling: Corrects scaffolding errors, resolves collapsed homozygous regions, and fills assembly gaps using unplaced sequences.
• Handling Complex Regions: Phases highly heterozygous and complex genomic regions that are challenging for other assembly methods.

Scientific Applications:

• Cross-taxa genome assembly: Applicable to plants, fungi, and animals for generating high-quality phased diploid genome assemblies.
• Evolutionary biology: Enables haplotype-resolved analyses required for studies of evolutionary relationships and population history.
• Genetics and comparative genomics: Supports genetic and comparative-genomics investigations that require detailed diploid and haplotype information.

Methodology:

Leverages genetic maps and genomes of related species to guide scaffolding of draft diploid assemblies, integrates sequences into phased pseudomolecules, performs quality control checks and report generation to detect and correct misassemblies, fills gaps using unplaced sequences, and resolves collapsed homozygous and highly heterozygous regions.