NanoSimFormer: an end-to-end Transformer-based nanopore signal simulator with basecaller guidance (opens in new tab)

AbstractMotivationHigh-fidelity simulation of nanopore sequencing signals is critical for rigorous benchmarking and validation of the nanopore signal processing pipeline. However, existing signal simulators often fail to capture the non-linear dynamics of nanopore current signals, relying on static pore models or lacking optimization objectives tied to basecalling, resulting in synthetic signals with low basecalling accuracy and fidelity.ResultsWe introduce NanoSimFormer, an end-to-end Transf...