Bream: an open-source deep learning framework for simultaneous base calling and DNA methylation detection on novel nanopore sequencing platforms

Nanopore sequencing enables the simultaneous detection of genetic sequences and DNA modifications, yet the development of accurate, open-source computational models for these tasks, particularly for non-ONT platforms, remains challenging. To address this, we developed Bream, an open-source deep learning framework that integrates a convolutional neural network with a reverse long short-term memory network for base calling and a bidirectional LSTM with an attention mechanism for methylation detection. We trained and evaluated Bream on datasets from A. thaliana, O. sativa , and D. melanogaster generated using a novel nanopore sequencing platform (Qitan Technology’s QCell-384) featuring engineered helicase and nanopore proteins. The framework achieved base-calling accuracies between 89.38% and 91.83%, comparable to ONT’s R9.4 platform, and demonstrated high-performance methylation detection, with an AUC-ROC of 0.98 on a D. melanogaster dataset. Furthermore, its estimates of whole-genome CpG methylation frequency showed strong agreement (Pearson’s r ≥ 0.96) with bisulfite sequencing data across species. These results demonstrate Bream as a powerful, transparent, and adaptable tool that facilitates simultaneous base calling and methylation detection on emerging nanopore sequencing platforms, thereby advancing open innovation in the field.