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Related Experiment Video

Updated: Jan 1, 2026

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Rup (RNA-seq Usability Assessment Pipeline) - Quality Control for Bulk RNA-seq Experiments in Eukaryotes

Published on: November 7, 2025

Transcriptome assembly from long-read RNA-seq alignments with StringTie2.

Sam Kovaka^1,2, Aleksey V Zimin^2,3, Geo M Pertea^2,3

¹Department of Computer Science, Johns Hopkins University, Baltimore, MD, 21218, USA.

|December 18, 2019

Summary

This summary is machine-generated.

StringTie2 is a new tool that assembles RNA sequencing data. It improves transcriptome assembly accuracy and speed for both long and short sequencing reads, enhancing data analysis.

Keywords:

Gene expression Long-read sequencing RNA-seq Transcriptome assembly

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Last Updated: Jan 1, 2026

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Published on: November 7, 2025

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Published on: May 28, 2021

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Published on: February 18, 2022

Area of Science:

Genomics
Bioinformatics

Background:

Single-molecule sequencing instruments generate long RNA reads (thousands of nucleotides).
Assembling long reads enhances the sensitivity of long-read analyses.

Purpose of the Study:

To present StringTie2, a novel reference-guided transcriptome assembler.
To improve transcriptome assembly using both long and short RNA sequencing reads.

Main Methods:

StringTie2 incorporates new algorithms to manage the high error rate in long reads.
It supports the use of full-length super-reads assembled from short reads for improved assembly quality.

Main Results:

StringTie2 demonstrates enhanced accuracy and speed compared to existing tools.
The assembler offers reduced memory usage in transcriptome analysis.

Conclusions:

StringTie2 provides a more efficient and accurate method for transcriptome assembly.
This tool advances the analysis of both long-read and short-read RNA sequencing data.