FusionSeq protocols

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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


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  • person_outline Mark Rubin <>
  • person_outline FusionSeq Team <>

Additional information


Publication for FusionSeq

FusionSeq in pipeline

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

[…] as sam files––were sorted so that two reads of each pair is in order of chromosomal location. the resulting sam files were converted into mrf format using rseqtools. with the mrf files as input, the fusionseq (version 0.6.1) pipeline was run with default parameters, until the part that calculates confidence estimates for fusion candidates. “abnormal insert size filter” and “small homology […]

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FusionSeq in publications

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 […]

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 […]

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 […]

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; […]

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 […]

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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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