Breakpointer is 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 break-points can indicate insertions longer than the read length and SVs located in repetitve regions which might be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.
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Bioinformatics. 2012 Apr 1;28(7):1024-5. Epub 2012 Feb 1.
Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA.