Hiruna Samarakoon, Yuk Kei Wan, Sri Parameswaran, Jonathan G��ke, Hasindu Gamaarachchi, Ira W Deveson
MOTIVATION: 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'. 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, analysis and interpretation. The process of transforming raw signal data into nucleotide sequences, known as basecalling, is a fundamental step in nanopore sequencing.
RESULTS: In this study, we leverage the move table produced by ONT's basecalling software to create a lightweight de novo k-mer model for RNA004 chemistry. We demonstrate the validity of our custom k-mer model by using it to guide signal-to-sequence alignment analysis, achieving high alignment rates (97.48%) compared to larger default models. Additionally, our 5-mer model exhibits similar performance as the default 9-mer models another analysis, such as detection of m6A RNA modifications. We provide our method, termed Poregen, as a generalisable approach for creation of custom, de novo k-mer models for nanopore signal data analysis.
AVAILABILITY AND IMPLEMENTATION: Poregen is an open source package under an MIT licence: https://github.com/hiruna72/poregen.
SUPPLEMENTARY INFORMATION: Supplementary Note 1.
