Yeh, Yang MingYang MingYehYI-CHANG LU2023-06-052023-06-052022-08-1513674803https://scholars.lib.ntu.edu.tw/handle/123456789/631791Motivation: MinION, a third-generation sequencer from Oxford Nanopore Technologies, is a portable device that can provide long-nucleotide read data in real-time. It primarily aims to deduce the makeup of nucleotide sequences from the ionic current signals generated when passing DNA/RNA fragments through nanopores charged with a voltage difference. To determine nucleotides from measured signals, a translation process known as basecalling is required. However, compared to NGS basecallers, the calling accuracy of MinION still needs to be improved. Results: In this work, a simple but powerful neural network architecture called multi-scale recurrent caller (MSRCall) is proposed. MSRCall comprises a multi-scale structure, recurrent layers, a fusion block and a connectionist temporal classification decoder. To better identify both short-and long-range dependencies, the recurrent layer is redesigned to capture various time-scale features with a multi-scale structure. The results show that MSRCall outperforms other basecallers in terms of both read and consensus accuracies.en[SDGs]SDG3journal article10.1093/bioinformatics/btac435357668082-s2.0-85136561519WOS:000823444300001https://api.elsevier.com/content/abstract/scopus_id/85136561519