In cancer, fusions are important diagnostic markers and targets for therapy. Long-read transcriptome sequencing allows the discovery of fusions with their full-length isoform structure. However, due to higher sequencing error rates, fusion finding algorithms designed for short reads do not work. Here we present JAFFAL, to identify fusions from long-read transcriptome sequencing. We validate JAFFAL using simulations, cell lines, and patient data from Nanopore and PacBio. We apply JAFFAL to single-cell data and find fusions spanning three genes demonstrating transcripts detected from complex rearrangements. JAFFAL is available at https://github.com/Oshlack/JAFFA/wiki.
CITATION STYLE
Davidson, N. M., Chen, Y., Sadras, T., Ryland, G. L., Blombery, P., Ekert, P. G., … Oshlack, A. (2022). JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biology, 23(1). https://doi.org/10.1186/s13059-021-02588-5
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