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

Research output: Contribution to journalArticlepeer-review

15 Scopus citations

Abstract

We developed Breakpointer, a fast algorithm to locate breakpoints of structural variants (SVs) from single-end reads produced by next-generation sequencing. 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 be missd by other methods. Thus, Breakpointer complements existing methods to locate SVs from single-end reads.

Original languageEnglish (US)
Article numberbts064
Pages (from-to)1024-1025
Number of pages2
JournalBioinformatics
Volume28
Issue number7
DOIs
StatePublished - Apr 2012
Externally publishedYes

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