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An efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions.

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(Ge et al., 2011) FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution. Bioinformatics.
PMID: 21593131

(Lin et al., 2014) Making the difference: integrating structural variation detection tools. Briefings in bioinformatics.
PMID: 25504367