ERG and prostate cancer: LongGF, while having high accuracy for detection of fusions with simulated data, surprisingly was found least effective here in consistently missing 4/16 control fusions, only one of which was missed in common with another method: TMPRSS2::ERG, the hallmark fusion of prostate cancer, missed by both LongGF and FusionSeeker, while CTAT-LR-fusion detects 45, 98, and 104 long isoform reads supporting TMPRSS2::ERG across the three sequenced libraries.