LiftoffTools

LiftoffTools automates the detection and analysis of gene sequence variants, synteny, and gene copy number changes between gene annotations mapped across genome assemblies.

Key Features:

• Gene Sequence Variant Analysis: Detects and analyzes gene sequence variants in protein-coding genes mapped between genome assemblies.
• Synteny Analysis: Analyzes gene synteny between mapped genome assemblies.
• Copy Number Analysis: Detects and analyzes gene copy number changes between mapped genome assemblies.
• Liftoff Integration: Leverages Liftoff for annotation transfer between genome assemblies of the same or closely related species.

Scientific Applications:

• Comparative Genomics: Compares genes mapped between two genome assemblies to identify biologically consequential differences in closely related genomes.
• Genome Assembly Comparison: Enables comparison of gene annotations mapped between different genome assemblies, such as two human genome assemblies.

Methodology:

LiftoffTools uses Liftoff for annotation transfer and provides modular analysis of the mapped annotations.