TRUP stems from my earlier ambition for a TRUE-pipeline for RNA-seq analysis in cancer samples. Due to the high dynamic range of gene expression levels, as well as various splicing pattern and gene fusions, transcriptomic information measured by RNA-seq is highly complex and bias-prone. The original purpose of TRUP is to

1) identification of fusion transcripts; 2) RNA-seq quality assesment; 2) Gene or exon-read counting. The fusion detection module in TRUP combines split-read/read-pair mapping with regional de-novo assembly to achieve a balance between sensitivity and precision.

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data, Genome Biology, 2015