JLOH

JLOH infers and analyzes loss of heterozygosity (LOH) blocks from genomic data to characterize allele loss and assign LOH blocks to their subgenomic origins in heterozygous and hybrid genomes.

Key Features:

• LOH inference: Infers LOH blocks by analyzing SNP density and read coverage across genomes.
• Input formats: Accepts reference genome FASTA, mapped reads BAM, and variant VCF files as input.
• SNP and segment detection: Detects LOH at single-nucleotide polymorphisms (SNPs) and extended DNA segments, including hemizygosity.
• SNP density metric: Uses SNP density (SNPs per kilobase) as a primary metric for identifying candidate LOH regions.
• Read coverage analysis: Integrates read coverage information across genomic positions to support LOH calls.
• Subgenome assignment: Assigns each identified LOH block to its respective subgenome of origin.
• Heterozygosity threshold: Designed to operate on genomes exhibiting substantial heterozygosity (≥1%), including hybrids.

Scientific Applications:

• Genetics: Characterizing allele loss and hemizygosity in genetic studies.
• Evolutionary biology: Studying LOH as a mechanism of evolutionary adaptation and genomic dynamics.
• Biodiversity conservation: Assessing genomic consequences of LOH in conservation genetics.
• Hybrid genome analysis: Resolving subgenomic architecture and LOH patterns in hybrid organisms.
• Speciation and adaptation: Investigating roles of heterozygosity loss in adaptation and speciation processes.

Methodology:

Uses reference FASTA, BAM, and VCF inputs to analyze SNP density (SNPs per kilobase) and read coverage across genomic positions to identify candidate LOH blocks and assign them to subgenomes.