RecoverY

RecoverY: k-mer-based Y Chromosome Read Classification and Assembly Optimization

RecoverY enhances assembly of the haploid mammalian Y chromosome by applying k-mer-based read classification to identify and select Y-specific reads from datasets characterized by high repeat content and low sequencing depth.

Key Features:

• Automated Parameter Selection: Automatically determines the k-mer abundance threshold defining Y-specific k-mers, eliminating manual parameter tuning.
• Integration of Prior Knowledge: Incorporates Y chromosome information from related species or known Y transcript sequences to improve Y-specific read identification accuracy.
• Robust Performance Across Datasets: Validated on simulated and real human and gorilla genome data, demonstrating stability across parameter variations.
• Improved Assembly Metrics: Achieves 33% increase in assembly size and 20% improvement in NG50 compared to read or contig filtering strategies.

Scientific Applications:

• Y-Chromosome Genomics: Supports accurate assembly for studies of genetic diversity, evolutionary biology, and sex chromosome-associated disease.

Methodology:

RecoverY classifies sequencing reads using k-mer abundance profiles to identify Y-specific sequences. Automatic threshold selection, guided by prior Y chromosome knowledge, refines discrimination of Y-derived reads within complex genomic datasets prior to assembly.