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

• Published in: Bioinformatics (Oxford, England) Vol. 28; no. 7; pp. 1024 - 1025
• Main Authors: RUPING SUN, LOVE, Michael I, ZEMOJTEL, Tomasz, EMDE, Anne-Katrin, CHUNG, Ho-Ryun, VINGRON, Martin, HAAS, Stefan A
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 01.04.2012
• Subjects: Algorithms; Biological and medical sciences; Computational Biology - methods; Fundamental and applied biological sciences. Psychology; General aspects; Genomic Structural Variation; Humans; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Sequence Analysis, DNA - methods; Breakpoint; Artefact; Mapping
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/bts064

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. https://github.com/ruping/Breakpointer ruping@molgen.mpg.de Supplementary material is available at Bioinformatics online.