#39 · Tools & infrastructure

Nanopore direct RNA sequencing benchmarks for detecting diverse RNA modifications

The dominant thread in this set is the evaluation of nanopore direct RNA sequencing for detecting RNA modifications. One bioRxiv preprint benchmarks ten tools for identifying rRNA modifications in Escherichia coli and reports that AUROC alone is insufficient as a performance measure. A published Nucleic Acids Research assessment systematically tests detection of therapeutic chemistries, including PS, 2'OMe, 2'F, LNA, 2'MOE, m1Ψ, m5C, 5moU and 5iodoC. What is new is the extension of direct RNA sequencing benchmarking from native rRNA modifications to therapeutic RNA modifications. ADAR-Sense is a distinct, design-oriented contribution: an open-access, species-agnostic web tool that automates ADAR-based sense-edit-switch RNA sensor design with user-tunable sensor length and mismatch parameters. It shares the RNA measurement and engineering focus of the set rather than a common model-evaluation framework.