ShortFuse specifications


Unique identifier OMICS_01355
Name ShortFuse
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A transcriptome
Output data RefSeq IDs, names of the two genes involved in the fusion, score field
Output format BEDPE
Operating system Unix/Linux
Programming languages C++, Python
License BSD 2-clause “Simplified” License
Computer skills Advanced
Stability Stable
Bowtie, GCC, NetworkX
Maintained Yes



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Publication for ShortFuse

ShortFuse in publication

PMCID: 3633050
PMID: 23815381
DOI: 10.1186/1471-2105-14-S7-S2

[…] last two years many chimera-detection tools have been developed and published. to the best of our knowledge, chimerascan [], defuse [], fusionfinder [], fusionhunter [], fusionmap [], mapsplice [], shortfuse [], tophat-fusion [] are the most commonly used tools for chimera detection. chimerascan and shortfuse were not considered here since their run did not terminate properly […]

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ShortFuse institution(s)
Bioinformatics and Systems Biology Program, University of California San Diego, La Jolla, CA, USA; Department of Pediatrics, University of California San Diego, La Jolla, CA, USA; Department of Genomic Medical Sciences, Kyoto Prefectural University of Medicine, Kyoto, Japan; Institute for Genomic Medicine, University of California San Diego, La Jolla, CA, USA
ShortFuse funding source(s)
This tool was funded by the National Institutes of Health (grant numbers RO1-HG004962, 5U54HL108460, 1R21CA152613-01, CTSA-1U54RR025204) and the California Institute for Regenerative Medicine (grant number DR1-01430).

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