Sequoia

Sequoia is a visual analytics tool to facilitate the interactive exploration of nanopore sequencing data, particularly long RNA reads obtained from direct-sequencing technologies like Oxford Nanopore's. By combining a Python-based backend with a multi-view visualization interface, Sequoia enables users to import raw nanopore sequencing data in Fast5 format, cluster sequences based on electric-current similarities, and drill down into signals to identify properties of interest.

The authors demonstrated the tool's effectiveness by analyzing approximately 500,000 reads from direct RNA sequencing data of the human HeLa cell line, focusing on comparing signal features from m6A and m5C RNA modifications. Through iterative visual exploration and adjustment of dimensionality reduction parameters, Sequoia allows users to separate modified RNA sequences from their unmodified counterparts and discover new, qualitative signal signatures that characterize these modifications.