Article

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

2025-08-28

Abstract excerpt

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 alternati...

Topics

Open a Topic to create a Post that cites this publication.

Identifiers and source

Literature Corpus work: 29a031fd-73e5-5eb1-a39f-90e9bd2f2fd7
DOI: 10.1101/2025.08.23.671926

Open publication

Related research

Semantic proximity does not establish scientific evidence.

Click a neighbor to travelStep 1 · 12 closest

Transcriptome Universal Single-isoform COntrol: A Framework for Evaluating Transcriptome reconstruction QualityDOI 10.1101/2025.08.23.671926Read

Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencingSemantic proximity Read

RATTLE: Reference-free reconstruction and quantification of transcriptomes from Nanopore sequencingSemantic proximity Read

SIRVs: Spike-In RNA Variants as External Isoform Controls in RNA-SequencingSemantic proximity Read

A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seqSemantic proximity Read

SCOTCH: isoform-level characterization of gene expression through long-read single-cell RNA sequencingSemantic proximity Read

Evaluating Methods for Differential Gene Expression And Alternative Splicing Using Internal Synthetic ControlsSemantic proximity Read

A technology-agnostic long-read analysis pipeline for transcriptome discovery and quantificationSemantic proximity Read

Systematic assessment of long-read RNA-seq methods for transcript identification and quantificationSemantic proximity Read

Selecting differential splicing methods: Practical considerations for short-read RNA sequencingSemantic proximity Read

A ratio-based framework using Quartet reference materials for integrating long- and short-read RNA-seqSemantic proximity Read

TRAWLING: a Transcriptome Reference Aware of spLIciNG eventsSemantic proximity Read

Accurate isoform quantification by joint short- and long-read RNA-sequencingSemantic proximity Read