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DescriptionBreakTrans maps gene fusions to genomic architecture in cancer cells
Development Information
Current version0.0.6
LicenseGPL v3
Last updated2013/02/13
Citation Chen, K., Navin, N.E., Wang, Y., et al. BreakTrans: uncovering the genomic architecture of gene fusions, Genome Biology v. 14 p R87 (2013) 
Help and Support
Contact Ken Chen 


BreakTrans is a computer program that maps predicted gene fusions to genomic structural rearrangements so as to validate both types of events and provide them mechanism/functional interpretation. It requires input from at least one gene fusion prediction program (such as Tophat-fusion, deFuse and BreakFusion) and at least one genomic breakpoint detection program (such as BreakDancer and CREST ).


The BreakTrans package includes two parts, executable files and annotation data files for each specific cancer. To run it, users need to download the executable files and the annotation database.

Executable Package (6.5 Kb)

Annotation database (184 Mb)

Test data set for breast cancer cell-line SK-BR-3 (673 Kb)