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Salmon

Salmon

A tool to quantify transcript expression in RNA-seq data. The Salmon algorithm can correct for GC-bias, and it uses 'selective-alignment' and massively-parallel stochastic collapsed variational inference to achieve high accuracy and speed. It reports transcripts per million mapped reads (TPM).

Topic

RNA-seq; Gene expression; Transcriptomics

Details

  • Operation: Sequence composition calculation; RNA-Seq quantification; Gene expression analysis
  • Input: FASTA, FASTQ, SAM, BAM
  • Output: -
  • Software interface: Command-line user interface
  • Language: C++
  • Operating system: Linux
  • License: GNU GPL v3
  • Cost: Free
  • Version name: 1.0.0
  • Maturity: Mature
  • Credit: the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative, the US National Science Foundation (NSF), the US National Institutes of Health (NIH), Alfred P. Sloan
  • Contact: Rob Patro rob.patro _at_ cs.stonybrook.edu | Carl Kingsford carlk _at_ cs.cmu.edu
  • Collection: -

Publications

Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C "Salmon provides fast and bias-aware quantification of transcript expression." Nat Methods. 2017 Apr;14(4):417-419. https://doi.org/10.1038/nmeth.4197
PMID: 28263959
PMCID: PMC5600148


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