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ScanMST

ScanMST: Detection of Multi-Segment Transcripts from Long Reads

A powerful tool for detecting Multi-segment transcripts (MSTs) with long reads and transcript segment graphs.

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Key Features

High Accuracy

Robust detection of multi-segment transcripts at base resolution.

Easy to Use

A streamlined CLI with sensible defaults—start running analyses.

Visualization-Ready JSON Output

Produce structured JSON files optimized for transcript segment graph visualization.

Quick Start

Get up and running with ScanMST in under 5 minutes:

# Install ScanMST
pip install scanmst

# Run ScanMST on your long-read rna-seq data
scanmst --input input_data.bam --ref ref.fasta --gtf annotation.gtf --output output_name

Ready to dive in? Check out our Quick Start Guide.

What is ScanMST?

ScanMST is a multi-segment transcript caller for third-generation sequencing reads. It is able to detect and classify the multi-segment transcripts with the following four forms of transcript segment links: ICRL, ICTL, ITPL, and ITTL (see the figure below).

Modeling segment connectivity

Citation

If you use ScanMST in your research, please cite:

@software{scanmst2026,
  title={Structural variation reshapes the transcriptome by generating pervasive multi-segment transcripts},
  author={Wang, Ting-You, Li, Yangyang, Liu, Qi and Yang, Rendong},
  year={2026},
  url={https://github.com/ylab-hi/ScanMST}
}

License

ScanMST is licensed under the GNU General Public License 3.0. See License for details.