Fusion gene discovery in single cells with LongFUSE from high throughput long read single cell transcriptomes

High throughput long-read single cell RNA sequencing allows for fusion gene discovery in thousands of cells in parallel, which however are constrained by the lack of robust computational tools. To address this, we develop LongFUSE that employs XOR logic gate and stringent filtering criteria for accurate detection of cell-specific fusion genes and their splicing isoforms. LongFUSE outperformed existing tools in both simulation and real data, demonstrating high accuracy and robustness.