DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

The MinION device by Oxford Nanopore produces very long reads (reads over 100 kBp were reported); however it suffers from high sequencing error rate. We present an open-source DNA base caller based on deep recurrent neural networks and show that the accuracy of base calling is much dependent on the underlying software and can be improved by considering modern machine learning methods. By employing carefully crafted recurrent neural networks, our tool significantly improves base calling accuracy on data from R7.3 version of the platform compared to the default base caller supplied by the manufacturer. On R9 version, we achieve results comparable to Nanonet base caller provided by Oxford Nanopore. Availability of an open source tool with high base calling accuracy will be useful for development of new applications of the MinION device, including infectious disease detection and custom target enrichment during sequencing.