Francisco J. Pardo-Palacios

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.

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

This paper introduces TranD, a tool for comparing transcriptome structures using nucleotide-level distance metrics to assess transcript complexity and structural differences between species or annotations.

SQANTI-SIM simulates controlled transcript novelty for long-read RNA-seq data to benchmark transcriptome reconstruction pipelines.

SQANTI characterizes long-read transcript sequences to assess quality and improve quantification of full-length transcriptomes.