svaRetro

svaRetro annotates non-reference retrotransposed transcripts and, together with the companion R package svaNUMT, annotates nuclear integrations of mitochondrial DNA (NUMTs) from structural variant calls to support interpretation of genomic structural variation.

Key Features:

• Annotation of Retrotransposed Transcripts: Identifies and annotates processed (retro-copied) transcripts integrated at novel genomic locations from structural variant calls.
• Nuclear Integration of Mitochondrial DNA (NUMT) Detection: Detects and annotates mitochondrial DNA segments transferred to the nuclear genome using the svaNUMT package.
• Modular R Package Design: Implemented as two modular R packages, svaRetro and svaNUMT, providing separate functionality for retrotransposition and NUMT annotation.
• Performance Evaluation: Validated using simulations and public benchmarking datasets to assess detection and annotation performance.
• Integration with Public Databases: Facilitates annotation of processed transcripts within public structural variant databases.

Scientific Applications:

• Genomic Research: Characterizes how retrotransposition and NUMTs contribute to genomic variation, evolution, and stability.
• Structural Variant Analysis: Supports interpretation of structural variant calls and identification of novel genetic elements and their potential functional impacts.

Methodology:

Uses a systematic computational approach that leverages algorithms to process sequencing data, detect and annotate non-reference retrotransposed transcripts, and employs specialized techniques to detect mitochondrial DNA segments integrated into the nuclear genome.