breakpointR

breakpointR detects strand-state changes and genomic breakpoints in aligned single-cell Strand-seq data and supports fine-mapping and global haplotype assembly within R/Bioconductor.

Key Features:

• Strand Directionality Analysis: Detects local changes in strand directionality in aligned Strand-seq data.
• Breakpoint Detection: Identifies genomic breakpoints associated with structural variations and rearrangements, including sister chromatid exchanges and germline inversions.
• Fine-Mapping Applications: Enables fine-mapping of strand-state changes to precisely localize breakpoint positions.
• Global Haplotype Assembly Support: Assists assembly of global haplotypes from Strand-seq data to support genome-wide haplotype reconstruction.

Scientific Applications:

• Sister Chromatid Exchange Mapping: Mapping exchanges between sister chromatids to study DNA repair mechanisms and chromosomal stability.
• Germline Inversion Analysis: Detecting germline inversions to inform studies of evolution and genetic disorders.
• Haplotype Assembly: Constructing haplotypes across large genomic regions for population genetics and disease-association studies.

Methodology:

Analyzes aligned Strand-seq reads to detect strand-state changes and breakpoints using breakpoint detection algorithms; implemented as an R/Bioconductor package.