Introduction

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/Breakpointer CONTACT: ruping@molgen.mpg.de SUPPLEMENTARY INFORMATION: Supplementary material is available at Bioinformatics online.

Publications

  1. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
    Cite this
    Sun R, Love MI, Zemojtel T, Emde AK, Chung HR, Vingron M, Haas SA, 2012-04-01 - Bioinformatics (Oxford, England)

Credits

  1. Ruping Sun
    Developer

  2. Michael I Love
    Developer

  3. Tomasz Zemojtel
    Developer

  4. Anne-Katrin Emde
    Developer

  5. Ho-Ryun Chung
    Developer

  6. Martin Vingron
    Developer

  7. Stefan A Haas
    Investigator

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Summary
AccessionBT001180
Tool TypeApplication
Category
PlatformsLinux/Unix
TechnologiesC++, Perl
User InterfaceTerminal Command Line
Download Count0
Submitted ByStefan A Haas