Same workflow
salmon index → salmon quant → quant.sf. Drop-in for tximport, tximeta,
fishpond, and swish.
salmon
Fast, accurate transcript-level quantification from RNA-seq reads — now a portable, single-binary Rust tool.
What is salmon?
Section titled “What is salmon?”salmon quantifies the expression of transcripts from RNA-seq data. It pairs a fast mapping stage — selective alignment or alignment-free sketch mode — with a statistical model of the sequencing experiment and an EM/VBEM optimizer to produce accurate transcript-level abundance estimates.
salmon 2.0 is a from-scratch Rust rewrite of the original C++ tool. It is faster, ships as a single portable binary, and is trivial to install — while keeping the same workflow and the same output formats your downstream tools already read.
Two mapping modes
Selective alignment for maximum accuracy, or --sketch for alignment-free
speed.
Easy to install
A single binary via the install script, cargo install, conda, or Docker —
no compiler or system libraries required.
Coming from C++ salmon?
See what changed in 2.0. The biggest one: rebuild your index.