ShortFuse statistics

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Citations per year

Number of citations per year for the bioinformatics software tool ShortFuse

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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




No version available


Publication for ShortFuse

ShortFuse citation


State of art fusion finder algorithms are suitable to detect transcription induced chimeras in normal tissues?

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

[…] wledge, 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 during the preliminary testing phase. Before describing fusion finder algorithms, we introduce the terms used in the rest […]

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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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