BreakSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BreakSeq

Tool usage distribution map

This map represents all the scientific publications referring to BreakSeq per scientific context
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Associated diseases


Popular tool citations

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BreakSeq specifications


Unique identifier OMICS_02168
Name BreakSeq
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes




No version available


  • person_outline Mark Gerstein
  • person_outline Jan Korbel

Publication for BreakSeq

BreakSeq citations


FusorSV: an algorithm for optimally combining data from multiple structural variation detection methods

Genome Biol
PMCID: 5859555
PMID: 29559002
DOI: 10.1186/s13059-018-1404-6

[…] arity (40%) with the 1000GP Phase 3 SV callset [, , ]. For Jaccard similarity, FusorSV outperformed all individual algorithms (40%) with MetaSV as the next best method (32%), followed by BreakDancer, BreakSeq2, LUMPY, DELLY, and Hydra (all near 20%).Fig. 4For duplication calls, GenomeSTRiP performed at 26% precision and 14% recall, while CNVnator performed at 22% precision and 3% recall. The MetaS […]


Functional Impact and Evolution of a Novel Human Polymorphic Inversion That Disrupts a Gene and Creates a Fusion Transcript

PLoS Genet
PMCID: 4591017
PMID: 26427027
DOI: 10.1371/journal.pgen.1005495
call_split See protocol

[…] SAMtools [], and then converted to fastq. Otherwise, the raw fastq files were downloaded, avoiding color-space sequences and exome reads. The reads were processed with a slightly modified version of BreakSeq [] as described previously []. Reads overlapping at least 10 bases of either side of a breakpoint were retained (regardless of their length), and only those mapping uniquely to an Inv or Std […]

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BreakSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT, USA; Genome Biology unit, European Molecular Biology Laboratory, Heidelberg, Germany; Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria; Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA; Terrence Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Banting and Best Department of Medical Research, University of Toronto, Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, Toronto, ON, Canada; Department of Computer Science, University of Toronto, Toronto, ON, Canada; European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, UK; Department of Computer Science, Yale University, New Haven, CT, USA
BreakSeq funding source(s)
Supported by the NIH, the AL Williams Professorship funds, and the European Molecular Biology Laboratory.

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