BreakSeq statistics

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Citations per year

Number of citations per year for the bioinformatics software tool BreakSeq
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Tool usage distribution map

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

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Popular tool citations

chevron_left Structural variant detection CNV detection NAHR detection chevron_right
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Protocols

BreakSeq specifications

Information


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

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Versioning


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Maintainers


  • person_outline Mark Gerstein
  • person_outline Jan Korbel

Publication for BreakSeq

BreakSeq citations

 (2)
library_books

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

2018
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 […]

call_split

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

2015
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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