Breakpointer

Breakpointer is a software tool that allows for the fast and accurate detection of structural variants (SVs) from single-end reads produced by next-generation sequencing. It scans the alignment of single-end reads to identify regions containing potential breakpoints, taking advantage of local non-uniform read distribution and misalignments created by SVs. Breakpointer is useful for locating SVs in repetitive regions and for detecting insertions longer than the read length.

Topic

Topic

Detail

  • Operation: Statistical calculation

  • Software interface: Command-line user interface

  • Language: C++;Perl

  • License: Not stated

  • Cost: Free

  • Version name: -

  • Credit: Max Planck Society.

  • Input: -

  • Output: -

  • Contact: rs3412@c2b2.columbia.edu

  • Collection: -

  • Maturity: -

Publications

  • Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads.
  • Sun R, et al. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. Breakpointer: using local mapping artifacts to support sequence breakpoint discovery from single-end reads. 2012; 28:1024-5. doi: 10.1093/bioinformatics/bts064
  • https://doi.org/10.1093/bioinformatics/bts064
  • PMID: 22302574
  • PMC: -

Download and documentation

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