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FusionSeq | A modular framework for finding gene fusions by analyzing paired-end RNA-sequencing data

Infers candidate fusion transcripts by analyzing paired-end RNA-Seq data. FusionSeq is a standalone software that allows users to detect known and novel fusions and prioritize the candidates thanks to several statistics. The application includes tools to summarize and integrate the results into a web browser for visualization as well as a function for determining exact sequences at breakpoint junctions.

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FusionSeq forum

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FusionSeq classification

FusionSeq specifications

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

FusionSeq distribution

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No versioning.

FusionSeq support

Maintainers

  • Mark Rubin <>
  • FusionSeq Team <>

Additional information

http://info.gersteinlab.org/FusionSeq_FAQ

Credits

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Publications

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

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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