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FusionSeq specifications


Unique identifier OMICS_01351
Name FusionSeq
Software type Application/Script, Package/Module
Interface Command line interface
Restrictions to use None
Biological technology Illumina, Life Technologies, Pacific Biosciences, Roche
Operating system Unix/Linux
Programming languages C
Computer skills Advanced
Version 0.6.1
Stability Stable
bowtie, Blat, GSL, BIOS, GD library, ROOT, Homo Sapiens Reference Genome
Maintained Yes


No version available


  • person_outline Mark Rubin
  • person_outline FusionSeq Team

Additional information


Publication for FusionSeq

FusionSeq citations


De novo assembly and characterization of breast cancer transcriptomes identifies large numbers of novel fusion gene transcripts of potential functional significance

BMC Med Genomics
PMCID: 5575902
PMID: 28851357
DOI: 10.1186/s12920-017-0289-7

[…] genes that may be drivers of breast cancer onset and/or progression []., currently available computational methods for chimeric transcript discovery such as tophat-fusion [], snowshoeftd [] and fusionseq [], typically rely upon reference genome mapping of short (50–75 bp) paired-end reads generated by the sequencing of both ends (5′- and 3′-) of an rna or cdna fragment. while these methods […]


Discovering and understanding oncogenic gene fusions through data intensive computational approaches

Nucleic Acids Res
PMCID: 4889949
PMID: 27105842
DOI: 10.1093/nar/gkw282

[…] further dissemination., in recent years, there has been a remarkably concerted effort to develop algorithms and tools for identifying gene fusions from sequencing data. the first dedicated software, fusionseq, was published in 2010 (); by the end of 2012, 15 other tools had been released. at present, we find 30 different methods for identifying gene fusions () (table ), with the contenders […]


Divergent clonal evolution of castration resistant neuroendocrine prostate cancer

Nat Med
PMCID: 4777652
PMID: 26855148
DOI: 10.1038/nm.4045

[…] levels, respectively. if erg fusion was detected at either dna, mrna, or protein level, the sample was considered positive. for other non-canonical and canonical fusion transcript detection, fusionseq was employed as previously described., to assess cyld deletion in tissues, we developed a dual-color fish assay consisting of a locus specific probe (rp11-327f22) plus reference probe […]


Functional characterization of BC039389 GATM and KLK4 KRSP1 chimeric read through transcripts which are up regulated in renal cell cancer

BMC Genomics
PMCID: 4422297
PMID: 25888189
DOI: 10.1186/s12864-015-1446-z

[…] expression patterns or functions in general, and in oncogenesis in particular, are poorly understood., we used paired-end rna-seq and a specifically designed computational data analysis pipeline (fusionseq) to nominate read-through events in a small discovery set of renal cell carcinomas (rcc) and confirmed them in a larger validation cohort., 324 read-through events were called overall; […]


Fusion Transcript Discovery in Formalin Fixed Paraffin Embedded Human Breast Cancer Tissues Reveals a Link to Tumor Progression

PLoS One
PMCID: 3984112
PMID: 24727804
DOI: 10.1371/journal.pone.0094202

[…] transcript. recently published fusions detected using rna-seq data have displayed this discrete expression pattern at acceptor fusion junction sites , . multiple bioinformatics approaches including fusionseq , defuse and tophat-fusion have used expression data in their pipelines and all these methods rely on the analysis of an individual subject. the cohort-based approach described […]


NTRK1 Fusion in Glioblastoma Multiforme

PLoS One
PMCID: 3960150
PMID: 24647444
DOI: 10.1371/journal.pone.0091940

[…] or progression of the fusion-bearing gbms., to search for novel gene fusions in gbm, we analyzed paired-end rna-seq data of 162 gbm patients, available through tcga . a subset of modules from the fusionseq pipeline was adopted to score potential fusions based on the number of “discordant read pairs.” the discordant read pairs are paired-end reads whose 5′ and 3′ reads map to different genes, […]

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FusionSeq institution(s)
Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA; Molecular Biophysics and Biochemistry Department, Yale University, New Haven, CT, USA; Department of Pathology and Laboratory Medicine, Weill Cornell Medical College, New York, NY, USA; Department of Urology, Weill Cornell Medical College, New York, NY, USA; Prognosys Biosciences, Inc., La Jolla, CA, USA; Institute for Computational Biomedicine, Weill Cornell Medical College, New York, NY, USA; Department of Computer Science, Yale University, New Haven, CT, USA
FusionSeq funding source(s)
Supported by the ‘Yale University Biomedical High-Performance Computing Center’ and NIH grant no. RR19895, a National Cancer Institute grant R01CA125612, a National Human Genome Research Institute grant 5R44HG004237, the Prostate Cancer Foundation, and the Breslin Foundation.

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