breakpointR

The software tool "breakpointR" is an R package designed to process and interpret single-cell strand-specific sequencing data generated through the Strand-seq technique. Its development is motivated by the need for computational tools that can effectively capture the strand-specific information inherent in Strand-seq data.
breakpointR is tailored to detect local changes in strand directionality within aligned Strand-seq data. Its primary functions include fine-mapping sister chromatid exchanges, identifying germline inversions, and supporting global haplotype assembly. The tool aims to address a broad spectrum of applications related to Strand-seq, enhancing the capabilities of existing tools and making this sequencing technique more accessible.