segment_liftover

segment_liftover remaps genome segments between assemblies while preserving segment continuity for comparative and integrative genomic analyses.

Key Features:

• Continuity-Preserving Remapping: Preserves contiguous segment boundaries during assembly conversion and avoids breaking large segments into smaller sub-segments.
• Approximate Locus Conversion: Employs approximate locus conversion to locate equivalent regions in the target assembly and maintain segment integrity.
• Automated Batch Processing: Processes large numbers of structural genome variation entries in batch to support high-throughput datasets.
• Comprehensive Logging: Produces detailed logs of remapping operations to track conversions and support reproducibility.

Scientific Applications:

• Copy Number Variation (CNV) Analysis: Preserves quantitative representation of CNVs across assemblies to support accurate CNV comparison and analysis.
• Comparative Genomics: Enables comparison of genomic segments between assemblies or species by maintaining consistent segment boundaries.
• Integrative Studies: Facilitates integration of datasets from multiple genome assemblies by conserving segment continuity during remapping.

Methodology:

Uses approximate locus conversion to remap entire segments rather than individual coordinates, reducing fragmentation of genomic regions during assembly conversion.