Magnipore: A Powerful Pipeline for Detecting RNA Modifications and Mutations

Oxford Nanopore Technologies (ONT) can sequence DNA and RNA directly without amplification. They use nanopores with sequencing sensors to measure the electrical currents of nucleotides passing through the pores. This method can detect modifications and mutations. Scientists use this method to study the coronavirus and its variants to better understand and control the COVID-19 pandemic.

RNA modifications affect the structure and function of RNAs in cells, including viral RNAs. However, there is a lack of training data to assign individual signals to specific modifications reliably. Scientists are developing machine-learning approaches to detect modifications. Differential sequencing signals can also be detected using comparative analysis.

We have developed Magnipore, a Python pipeline that compares the raw sequencing signal of two ONT samples across alignable genomic regions of given reference sequences. It predicts global differential signals and classifies them as mutations or modifications. This tool can help study differential modifications and mutations between RNAs to better understand viral infections and develop treatments. We used Magnipore to compare SARS-CoV-2 samples and identified 55 detected mutations and 15 sites that hint at differential modifications between Alpha and Delta variants.

Jannes Spangenberg, Christian Höner zu Siederdissen, Milena Žarković, Sandra Triebel, Ruben Rose, Christina Martínez Christophersen, Lea Paltzow, Mohsen M. Hegab, Anna Wansorra, Akash Srivastava, Andi Krumbholz, Manja Marz: Magnipore: Prediction of differential single nucleotide changes in the Oxford Nanopore Technologies sequencing signal of SARS-CoV-2 samples. In: bioRxiv, 2023.