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bioRxiv · 10.1101/2021.12.20.471615

MSRCall: A Multi-scale Deep Neural Network to Basecall Oxford Nanopore Sequences

Yeh, Y.-M.·Lu, Y.-C.
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Abstract

AO_SCPLOWBSTRACTC_SCPLOWMinION, 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 the nucleotides from the 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. In this work, a simple but powerful neural network architecture called MSRCall is proposed. MSRCall comprises a multi-scale structure, recurrent layers, a fusion block, and a CTC decoder. To better identify both short-range 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.

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Yeh, Y.-M., Lu, Y.-C.. 2021-12-21. MSRCall: A Multi-scale Deep Neural Network to Basecall Oxford Nanopore Sequences. https://doi.org/10.1101/2021.12.20.471615

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