Salmon —Don't count . . . quantify!


Salmon is a tool for quantifying the expression of transcripts using RNA-seq data. Salmon uses new algorithms (specifically, coupling the concept of quasi-mapping with a two-phase inference procedure) to provide accurate expression estimates very quickly (i.e. wicked-fast) and while using little memory. Salmon performs its inference using an expressive and realistic model of RNA-seq data that takes into account experimental attributes and biases commonly observed in real RNA-seq data.


  • NSF BIO-1564917, CCF-1256087, CCF-1053918, EF-0849899
  • NIH 1R21HG006913, 1R21AI085376, 1R01HG005220, 5T32CA009337-35
  • Alfred P. Sloan Foundation Sloan Research Fellowship to Carl Kingsford

This material is based upon work supported by the National Science Foundation under Grant Numbers EF-0849899, IIS-0812111, CCF-1053918. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.