Alejandro Paniagua

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

SQANTI-browser converts SQANTI3 classifications into UCSC Genome Browser Track Hubs for visualizing and curating long-read transcriptomes with metadata and filtering capabilities.

This study compares two strategies for combining biologically replicated long-read RNA-seq data to identify transcripts, finding that 'Join & Call' is better for novel isoforms while 'Call & Join' is more efficient for large datasets.

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.