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TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.

Tianyuan Liu1,2, Alejandro Paniagua1,2, Fabian Jetzinger1,2,3

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Summary
This summary is machine-generated.

A new benchmarking framework, TUSCO, improves transcriptome analysis for long-read sequencing (LRS). It provides accurate quality control without external controls, overcoming limitations of current methods.

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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • Long-read sequencing (LRS) offers comprehensive transcriptome analysis but faces challenges like sequencing errors and biases.
  • Existing benchmarking tools (BUSCO, SIRVs, ERCCs) have limitations in accuracy and real-world sample complexity representation.
  • Simulation algorithms struggle to fully capture the complexity of actual biological samples.

Purpose of the Study:

  • To introduce the Transcriptome Universal Single-isoform COntrol (TUSCO) benchmarking framework for LRS transcriptome analysis.
  • To establish a reliable internal ground truth using a curated gene set lacking alternative isoforms.
  • To enhance the accuracy and reliability of transcriptome reconstruction quality control.

Main Methods:

  • Developed the TUSCO framework utilizing a curated gene set of single-isoform genes as an internal ground truth.
  • Quantified precision by detecting reconstructed transcripts deviating from reference annotations.
  • Assessed sensitivity by verifying detection completeness in human and mouse samples.
  • Created a TUSCO-novel challenge to evaluate the reconstruction of unannotated isoforms.

Main Results:

  • TUSCO metrics provide accurate and reliable transcriptome benchmarking without external controls.
  • The framework effectively addresses limitations of existing methods like BUSCO and spike-ins.
  • Demonstrated improved quality control standards for LRS transcriptome reconstruction.

Conclusions:

  • TUSCO offers a robust solution for benchmarking LRS transcriptome data.
  • The framework enhances the reliability of transcriptome reconstruction and quality control.
  • TUSCO significantly advances the field of transcriptome analysis using long-read sequencing.