RelocaTE2

RelocaTE2 maps transposable element (TE) insertion sites from population resequencing data with single base pair resolution to detect TE polymorphisms and target site duplications (TSDs).

Key Features:

• High sensitivity and specificity: Detects TE insertion sites in repetitive genomic sequences by utilizing reads associated with TEs as seeds to cluster read pairs on chromosomes.
• Single base pair resolution: Identifies target site duplications (TSDs) from alignments within each cluster for high-resolution mapping of TE polymorphisms.
• Comprehensive TE processing: Processes all TEs in a single cycle, enabling detection of polymorphisms across thousands of TEs within an individual genome or large population.
• Robust performance on varied data: Demonstrates high performance on both simulated and real sequence data, particularly with adequate sequence coverage.
• Applicability to light-coverage data: Identifies TE insertion sites using light coverage genome sequencing data for genotype analysis in population studies.

Scientific Applications:

• TE polymorphism discovery: Mapping of TE insertion sites and TSDs to characterize TE polymorphisms within and between populations.
• Population genetics and resequencing studies: Genotyping TE insertions across individuals in population resequencing projects, including light-coverage datasets.
• Study of TE impacts on genomes: Investigating contributions of TEs to gene regulation and genetic diversity across species.

Methodology:

RelocaTE2 uses reads associated with TEs as seeds to cluster read pairs on chromosomes, identifies TSDs from alignments within each cluster, and processes all TEs in a single cycle.