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We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing (NGS). By taking advantage of local non-uniform read distribution and misalignments created by SVs, Breakpointer scans the alignment of single-end reads to identify regions containing potential breakpoints. The detection of such breakpoints can indicate insertions longer than the read length and SVs located in repetitve regions which mightdoi:10.1093/bioinformatics/bts064 pmid:22302574 fatcat:q6w66jihczdzbg7wbxp6v7qlxe