# STAR and Salmon (RNA-seq alignment and quantification)

Source: https://onco.cc/terms/star-salmon/  
OnCo record `star-salmon` (Term). Data CC BY-NC 4.0, attribute "Data from OnCo (onco.cc)"; commercial use needs a licence.

## TL;DR

STAR lines sequencing reads up against the genome and Salmon estimates how much of each transcript is present; they are the two most common first steps of an RNA-seq pipeline.

## Summary

STAR (Spliced Transcripts Alignment to a Reference) is the ultrafast universal RNA-seq aligner described by Dobin and colleagues and used by the GDC pipeline; Salmon, from Patro and colleagues, quantifies transcript expression quickly and with correction for sequence and GC bias, using a lightweight mapping rather than full alignment. Which tool, genome build and annotation were used are provenance fields a model's training data should record, because they change the numbers.

## Fields

- Kind: Term
- Last checked: 2026-09-24
- Also known as: STAR aligner; STAR RNA-seq aligner; Salmon quantification; Salmon quantifier; pseudoalignment
- Tags: cansim-terms

## Notes

- Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/star-salmon.

## Sources

- STAR on GitHub (alexdobin/STAR): https://github.com/alexdobin/STAR
- Dobin et al., STAR: ultrafast universal RNA-seq aligner (Bioinformatics 2013): https://doi.org/10.1093/bioinformatics/bts635
- Salmon documentation: https://salmon.readthedocs.io/en/latest/
- Patro et al., Salmon (Nature Methods 2017): https://doi.org/10.1038/nmeth.4197

## Connected records

- technologies: [Clinical NGS bioinformatics and variant interpretation](https://onco.cc/technologies/ngs-bioinformatics-software/)
- terms: [Bulk RNA sequencing (RNA-seq) and the full transcriptome](https://onco.cc/terms/bulk-rna-seq/), [Cancer AI vocabulary (CanSim terms map)](https://onco.cc/terms/cancer-ai-vocabulary/), [Genome builds: GRCh38 versus hg19 (GRCh37)](https://onco.cc/terms/genome-builds/), [TPM, FPKM and raw counts (expression units)](https://onco.cc/terms/tpm-fpkm-counts/)

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