SQANTI-browser: visualization and curation of SQANTI3-classified long-read transcriptomes within the UCSC Genome Browser
Paniagua, A.; Blanco-Gomez, C.; Colomer Fernandez, A.; Diekhans, M.; Conesa, A.; Monzo, C.
Show abstract
Long-read sequencing enables transcriptome-wide isoform discovery. However, it generates substantial technical and structural ambiguity that complicates transcript interpretation. Here, we present SQANTI-browser, a classification-aware visualization framework that converts SQANTI3 outputs into interactive UCSC Genome Browser Track Hubs, preserving full transcript structural metadata. By integrating SQANTI classifications directly within the UCSC ecosystem, SQANTI-browser enables dynamic filtering and evidence-guided curation alongside public resource tracks. Furthermore, its adaptive architecture natively supports non-reference genomes, orthogonal data, and custom metadata fields. Applied to clinical, noisy, and synthetic datasets, SQANTI-browser resolves alignment artifacts and rescues actionable novel isoforms, providing a robust framework for long-read transcriptome curation.
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