Transcriptome Universal Single-isoform COntrol: A Framework for Evaluating Transcriptome Reconstruction Quality

Long-read sequencing (LRS) platforms, such as Oxford Nanopore and Pacific Biosciences, enable comprehensive transcriptome analysis but face challenges such as sequencing errors, sample quality variability, and library preparation biases. Current benchmarking approaches address these issues insufficiently: BUSCO assesses transcriptome completeness using conserved single-copy orthologs but can misinterpret alternative splicing as gene duplications, while spike-ins (SIRVs, ERCCs) oversimplify real- sample complexity, neglecting RNA degradation and RNA extraction artifacts, thus inflating performance metrics. Simulation algorithms are limited to recapitulate this complexity. To overcome these limitations, we introduce the Transcriptome Universal Single-isoform Control (TUSCO), a curated internal reference set of genes lacking alternative isoforms. TUSCO evaluates precision by identifying transcripts deviating from reference annotations and assesses sensitivity by verifying detection completeness in human and mouse samples. Masking TUSCO transcripts—and optionally inserting decoy splice variants—creates a ‘novel- isoform’ challenge that assesses recovery of the true, now-unannotated isoforms. Our validation demonstrates that TUSCO provides accurate and reliable benchmarking without external controls, significantly improving quality control standards for transcriptome reconstruction using LRS. ### Competing Interest Statement AC has received in-kind funding from Pacific Biosciences AC and TL are partners with Oxford Nanopore in MSCA-DN LongTREC project. Maria Curie-Skłodowska Actions, GA 101072892 Spanish Ministry of Science, PID2023-152976NB-I00 Spanish Ministry of Universities, FPU21/01597