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

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Sun,  Ruping
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Love,  Michael
IMPRS for Computational Biology and Scientific Computing - IMPRS-CBSC (Kirsten Kelleher), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Zemojtel,  Tomas
Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Emde,  Anne-Katrin
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Chung,  Ho-Ryun
Computational Epigenetics (Ho-Ryun Chung), Independent Junior Research Groups (OWL), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Vingron,  Martin
Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Haas,  Stefan
Gene Structure and Array Design (Stefan Haas), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society;

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Citation

Sun, R., Love, M., Zemojtel, T., Emde, A.-K., Chung, H.-R., Vingron, M., et al. (2012). Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Bioinformatics, 28(7), 1024-1025. doi:10.1093/bioinformatics/bts064.


Cite as: https://hdl.handle.net/11858/00-001M-0000-0014-7B7B-B
Abstract
Summary: 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.Availability: https://github.com/ruping/BreakpointerContact: ruping@molgen.mpg.deSupplementary information: Supplementary material is available at Bioinformatics online.