DiscoverY

DiscoverY identifies Y-chromosomal contigs in whole-genome assemblies using a k-mer-based hybrid approach that integrates proportion sharing with female references and depth-of-coverage analysis of male reads to improve precision and recall.

Key Features:

• k-mer-based classification: Uses k-mer comparisons as the basis for identifying Y-specific sequences.
• Proportion sharing with female references: Incorporates proportion sharing metrics with female genomic data to flag contigs absent or underrepresented in females.
• Depth-of-coverage analysis from male reads: Integrates male read depth information to differentiate Y-chromosomal sequences without requiring high-depth female sequencing.
• Hybrid dual-strategy framework: Combines proportion sharing and depth-of-coverage approaches to mitigate limitations of each method when used alone.
• Works with draft references or raw female reads: Operates using draft female references or raw sequencing reads from females when complete references are unavailable.
• Evaluated on multiple species: Performance was assessed on human and gorilla genomes.
• Supports multiple sequencing platforms: Demonstrated with Illumina, 10X Genomics, and PacBio sequencing data.
• Quantified performance metrics: Reported improvements in precision and recall and quantified the impact of using draft references or raw female reads.
• Limitations on X-homologous regions: Regions homologous to the X chromosome remain challenging to detect accurately.

Scientific Applications:

• Y chromosome research: Enables isolation of Y-specific contigs to support studies of sex determination and male fertility.
• Comparative genomics: Facilitates comparative analyses of Y-chromosomal sequence content across species such as human and gorilla.
• Assembly characterization: Supports identification of Y-derived contigs within whole-genome assemblies for downstream genomic analyses.

Methodology:

DiscoverY applies a k-mer-based dual-strategy combining proportion sharing with female genomic data and depth-of-coverage analysis from male reads to classify contigs as Y-chromosomal.