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deFuse | An algorithm for gene fusion discovery in tumor RNA-Seq data

Allows gene fusion discovery using RNA-Seq data. Defuse’s aim is to guide a dynamic programming-based split read analysis with discordant paired end alignments. The software employs heuristic filters to reduce the number of false positives and produces a fully annotated output for each predicted fusion. It was applied to ovarian tumours and sarcomas from the OvCaRe (Ovarian Cancer Research) frozen tumor bank.

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deFuse forum

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deFuse classification

deFuse specifications

Unique identifier:
OMICS_01345
Interface:
Command line interface
Input format:
FASTQ
Operating system:
Unix/Linux
Computer skills:
Advanced
Maintained:
Yes
Software type:
Package/Module
Restrictions to use:
None
Output format:
TSV
Programming languages:
C++
Stability:
Stable

deFuse distribution

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deFuse support

Documentation

Maintainer

  • Sohrab P. Shah <>

Additional information

https://sourceforge.net/projects/defuse

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Publications

Institution(s)

Centre for Translational and Applied Genomics, BC Cancer Agency, Vancouver, BC, Canada; School of Computing Science, Simon Fraser University, Burnaby, BC, Canada; Canada’s Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, BC, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada; Department of Molecular Oncology, BC Cancer Agency, Vancouver, BC, Canada

Funding source(s)

Supported by grants from the British Columbia Cancer Foundation and the Vancouver General Hospital Foundation, Genome Canada, the Michael Smith Foundation for Health Research, the Canadian Breast Cancer Foundation and the Canadian Institutes of Health Research’s Bioinformatics Training Program.

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