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BreakFusion specifications


Unique identifier OMICS_01342
Name BreakFusion
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data One or a set of whole transcriptome files that contains mapped paired-end RNA-seq reads.
Input format BAM
Output data Junctions.
Operating system Unix/Linux
Programming languages C++, Perl
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available


  • person_outline Ken Chen
  • person_outline Li Ding

Publication for BreakFusion

BreakFusion citations


Integrated genomic and molecular characterization of cervical cancer

PMCID: 5354998
PMID: 28112728
DOI: 10.1038/nature21386

[…] analysis was performed to identify putative driver fusions using both WGS (low-pass and high-coverage) and RNA-seq data. RNA-seq data for 178 Core Set cases were analyzed using the TopHat-Fusion and BreakFusion, PRADA, and MapSplice algorithms. To identify structural variations in WGS data, 50 low-pass WGS and 19 high-pass WGS samples were analyzed. Detection of structural variations in low-pass […]


Comparative assessment of methods for the fusion transcripts detection from RNA Seq data

Sci Rep
PMCID: 4748267
PMID: 26862001
DOI: 10.1038/srep21597

[…] Bellerophontes, BreakFusion, Chimerascan, nFuse, EricScript, FusionCatcher, FusionHunter, FusionMap, JAFFA, MapSplice, SOAPfuse, and TopHat-Fusion packages were downloaded and installed on our server (http://uvacse.v […]


Detection of a Distinctive Genomic Signature in Rhabdoid Glioblastoma, A Rare Disease Entity Identified by Whole Exome Sequencing and Whole Transcriptome Sequencing123

Transl Oncol
PMCID: 4562980
PMID: 26310374
DOI: 10.1016/j.tranon.2015.05.003

[…] wn bases or low quality bases, the remaining reads were aligned with the human reference genome (UCSC hg19). To find fusion transcripts, we utilized three types of fusion discovery software: deFuse , BreakFusion , and ChimeraScan . UniGene clusters were downloaded from the National Center for Biotechnology Information ( to assist in locating potential gene fusions. To […]


Clonal Evolution Revealed by Whole Genome Sequencing in a Case of Primary Myelofibrosis Transformed to Secondary Acute Myeloid Leukemia

PMCID: 4374044
PMID: 25252869
DOI: 10.1038/leu.2014.289

[…] pt abundance estimates are expressed in fragments per kilobase of exon per million fragments mapped (FPKM), as proposed by Mortazavi et al.() Gene fusions were detected from RNA sequencing data using BreakFusion version 1.0.() […]


Next generation sequencing in cancer research and clinical application

PMCID: 3599179
PMID: 23406336
DOI: 10.1186/1480-9222-15-4

[…] Cufflinks [,] and MISO [] construct a likelihood model that best explains all the reads obtained in the experiment. In addition, fusion transcripts can be detected using SOAPfusion, TopHat-Fusion [], BreakFusion [], FusionHunter [], deFuse [], FusionAnalyser [], etc. To obtain a more complete view of cancer genome, an integrative approach to study diverse mutations, transcriptomes and epigenomes s […]


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BreakFusion institution(s)
Department of Bioinformatics and Computational Biology, UT MD Anderson Cancer Center, Houston, TX, USA; The Genome Institute, St Louis, MO, USA; Department of Genetics, Washington University, St Louis, MO, USA; Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Internal Medicine, Division of Oncology, Washington University, St Louis, MO, USA
BreakFusion funding source(s)
Supported by The Cancer Center Support Grant from NCI (P30 CA016672); Center for Large-Scale Genome Sequencing and Analysis from NHGRI (U54 HG003079); Structural Genomic Variation analysis for the 1000 Genome project from NHGRI (U01 HG005209).

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