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bioRxiv · 10.1101/2024.06.30.601452

Leveraging Basecaller's Move Table to Generate a Lightweight k-mer Model

Samarakoon, H.·Kei Wan, Y.·Parameswaran, S.·Göke, J.·Gamaarachchi, H.·Deveson, I. W.
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Abstract

Nanopore sequencing by Oxford Nanopore Technologies (ONT) enables direct analysis of DNA and RNA by capturing raw electrical signals. Different nanopore chemistries have varied k-mer lengths, current levels, and standard deviations, which are stored in k-mer models. Particularly in cases where official models are lacking or unsuitable for specific sequencing conditions, tailored k-mer models are crucial to ensure precise signal-to-sequence alignment and interpretation. The process of transforming raw signals into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing. In this study, we leverage the basecallers move table to create a lightweight denovo k-mer model for RNA004 chemistry. We showcase the effectiveness of our custom k-mer model through high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models in m6A methylation detection.

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Samarakoon, H., Kei Wan, Y., Parameswaran, S., Göke, J., Gamaarachchi, H., Deveson, I. W.. 2024-07-01. Leveraging Basecaller's Move Table to Generate a Lightweight k-mer Model. https://doi.org/10.1101/2024.06.30.601452

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