findZX

findZX detects and visualizes sex chromosomes from whole-genome sequencing data by analyzing differences in genome coverage and heterozygosity between male and female samples using an automated Snakemake-based pipeline.

Key Features:

• Automated detection: Utilizes variations in genome coverage and heterozygosity to identify sex chromosomes.
• Snakemake-based workflow: Implements an automated Snakemake pipeline for reproducible analyses.
• Sample-number flexibility: Processes data from any number of male and female samples to accommodate diverse study designs.
• Lift-over and synteny: Provides genome coordinate lift-over to reference genomes and supplies synteny information to inspect sex-linked regions across larger contiguous chromosome segments.
• Scalability: Adaptable to a range of computational environments and capable of accommodating large datasets.
• Phylogenetic robustness: Demonstrated effectiveness across mammals, birds, reptiles, fish, and insects and over evolutionary distances greater than 80 million years.

Scientific Applications:

• Sex chromosome evolution studies: Identifies sex-linked regions to support analyses of sex chromosome diversity and evolutionary mechanisms.
• Population genomics: Detects undetected sex chromosome variation to help avoid misinterpretations in population genomic patterns.
• Comparative genomics: Enables cross-species comparisons via lift-over and synteny information to investigate evolutionary relationships and chromosomal conservation.

Methodology:

Analyzes differences in genome coverage and heterozygosity between male and female samples within an automated Snakemake pipeline and offers genome coordinate lift-over to map sex-linked regions onto reference genomes, providing synteny information.