Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads

Ruping Sun, Michael I. Love, Tomasz Zemojtel, Anne-Katrin Emde, Ho-Ryun Chung, Martin Vingron, Stefan A. Haas
2012 Computer applications in the biosciences : CABIOS  
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 might
more » ... missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads. Availability: Contact:
doi:10.1093/bioinformatics/bts064 pmid:22302574 fatcat:q6w66jihczdzbg7wbxp6v7qlxe