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Despite recent progress, computational tools that identify gene fusions from next-generation whole transcriptome sequencing data are often limited in accuracy and scalability. Here, we present a software package, BreakFusion that combines the strength of reference alignment followed by read-pair analysis and de novo assembly to achieve a good balance in sensitivity, specificity and computational efficiency. Availability: http://bioinformatics.mdanderson.org/main/BreakFusiondoi:10.1093/bioinformatics/bts272 pmid:22563071 pmcid:PMC3389765 fatcat:lqcrkcifwzaslch7oltqtzkw74