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StringTie

Definition
AI-generated

StringTie is a transcript assembler that reconstructs gene models and isoforms from spliced RNA-seq alignments using a network-flow formulation, and can quantify expression per transcript.

Topics
Sequencing and omics tech
URL
https://ccb.jhu.edu/software/stringtie/
Related
Genome Annotation Long-Read RNA-seq RNA Sequencing (RNA-seq)

Why it matters in GWAS

Custom or tissue-specific transcriptomes built with StringTie can change which isoforms are quantified for eQTL mapping or TWAS training compared with static GENCODE catalogs. Reporting the assembly method and reference annotation version is necessary for reproducibility.

Example usage

"We requantified gene and isoform expression with StringTie on HISAT2 alignments before cis-eQTL mapping."

Genome Annotation Long-Read RNA-seq RNA Sequencing (RNA-seq) Transcript Assembly
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Pertea M, et al. (2015). StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol.
  • Kovaka S, et al. (2019). Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol.
  • Ji HJ, Pertea M, Salzberg SL. (2026). Annotating genomes at increased scale and resolution. Nat Rev Genet. https://doi.org/10.1038/s41576-026-00937-3
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