BreakSeq protocols

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BreakSeq statistics

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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



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  • person_outline Mark Gerstein <>
  • person_outline Jan Korbel <>

Publication for BreakSeq

BreakSeq in pipeline

PMCID: 4690232
PMID: 26705468
DOI: 10.1186/s13742-015-0103-4

[…] a deletion instead (fig. )., we characterize the formation mechanism of a variant according to the pattern of repeats in and around the variant sequence using a classification scheme similar to the breakseq method [] and the 1000 genomes project approach []. briefly, we align the variant allele sequences to repbase using repeatmasker [] and perform reciprocal alignment between the left […]

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BreakSeq in publications

PMCID: 5655481
PMID: 29065176
DOI: 10.1371/journal.pone.0186721

[…] or microhomology-mediated break-induced repair (mmbir) []; 3) transposable element insertions (tei) []; and 4) expansion or contraction of variable numbers of tandem repeats (vntr) []. using the breakseq analysis pipeline [], we studied the formation mechanisms of all 33,628 deletions in the precise set (). in total, the formation mechanisms of 33,482 deletions were successfully inferred (). […]

PMCID: 4812662
PMID: 27025496
DOI: 10.1186/s12864-016-2589-2

[…] determine the formation mechanisms of the entire cnv dataset. with the benefit of single base-pair resolution, the relative contribution of each mutational mechanism can be defined. we applied the breakseq pipeline, which scans specific diagnostic sequence signatures at breakpoint junctions to infer the formation mechanism of each cnv []. eventually, 52.98 % (4,872) and 44.28 % (4,072) […]

PMCID: 4690232
PMID: 26705468
DOI: 10.1186/s13742-015-0103-4

[…] []., in this study, we revised and extended the previous framework by integration of several novel machine-learning methods (fig. , additional file : figure s1). in addition, we re-compiled the breakseq schemes for annotation of the ancestral state and formation mechanism of the identified structural variants and novel sequences []. in sum, we developed a single software package, asmvar, […]

PMCID: 4591017
PMID: 26427027
DOI: 10.1371/journal.pgen.1005495

[…] 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 […]

PMCID: 4585973
PMID: 26412485
DOI: 10.1038/srep14493

[…] variation allows us to compare the performance of several popular sv detection algorithms at a whole genome scale on real data. we compared lumpy, delly, metasv, pindel, breakdancer, cnvnator and breakseq2. compares all tools for deletion svs. we only considered svs greater or equal to 100 bp since both lumpy and delly were limited to that range. we were also careful to remove venter […]

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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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