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Table 1 A comparison of fusion detection performance on simulated RNA-Seq, 75 bp simulation of 50 fusions

From: JAFFA: High sensitivity transcriptome-focused fusion gene detection

Tool True positives Sensitivity False positives
JAFFA - Hybrid 44 (32/12/0) 88% 0
JAFFA - Assembly 39 (28/11/0) 78% 0
SOAPfuse 37 74% 1
JAFFA - Direct 34 (32/2/0) 68% 0
deFuse 34 68% 0
TopHat-Fusion 27 54% 0
FusionCatcher Unable to run on a low number of reads
  1. We ran all three modes of JAFFA in addition to SOAPfuse, TopHat-Fusion, deFuse and FusionCatcher on a simulation set of 57,000 75 bp RNA-Seq read pairs provided with FusionMap. JAFFA had the highest sensitivity when run in Hybrid mode, identifying 44 out of 50 possible fusion events. For all JAFFA modes, no false positives were reported. In parenthesis we show the value at each of JAFFA’s classification levels: (high/medium/low) confidence.