Salmon
Salmon quantifies the expression of transcripts using RNA-seq data. Salmon employs an algorithm that combines a quasi-mapping concept with a two-phase inference procedure to quickly provide accurate expression estimates. These inferences use an expressive and realistic model of RNA-seq data that take into account experimental attributes and biases commonly observed in real RNA-seq data.
Salmon is used to quantify expression of annotated transcripts in each sample. It then aggregates transcript-level estimates to gene-level estimates.
For more information, see combine-lab.github.io/salmon.