Genome-guided generative adversarial learning enables nanopore adaptive sequencing.

Abstract

Nanopore adaptive sequencing enables real-time target enrichment, yet current deep-learning methods require costly, sample-specific experimental training data. To address this, we developed GANBase, a genome-guided generative adversarial learning framework, which is trained exclusively on reference sequences and incorporates a Monte Carlo Tree Search-based Rollout strategy for model training. GANBase demonstrates robust performance in target enrichment and host depletion across diverse scenarios. In live adaptive sequencing experiments, it remains effective despite significant pore loss or flow cell version updates, providing a data-independent solution that significantly expands the utility of real-time targeted sequencing.