Comparison between TRUP and other publically available fusion detection tools. (a) Feature comparison: TRUP adopts breakpoint assembly after a sensitive detection of potential fusion points. Note that only TRUP and TopHat-Fusion are integrated into regular RNA-seq analysis pipelines, that is, the mapping results are shared for fusion detection and regular RNA-seq analysis. Alternative tools adopt various split-read mapping strategy specifically for fusion detection, generating customized mapping results, which could not be easily re-used for other purposes. (b) Computing resources consumed by TRUP and other tools for processing the data of sample S00054: resources used in the step of mapping are isolated for each tool to indicate the cost only for fusion detection and further processing (excl.: excluding). TRUP* indicates that TRUP is run with STAR as the mapper instead of GSNAP. (c) A heatmap showing the number of non-redundant reads spanning fusion-points for candidates predicted by at least two tools in sample S00054 (referred to as ‘shared fusions’ which is used as a gold set for evaluation). TRUP* indicates that TRUP is run with STAR as the mapper instead of GSNAP. Underlined fusions are experimentally validated.