Accurate, fast, and model-aware transcript expression quantification with Salmon

We wrote about Sailfish, Kallisto and Salmon extensively in the past. Readers will be happy to read Rob Patro et al.’s latest biorxiv paper discussing the arrival of Salmon-

Existing methods for quantifying transcript abundance require a fundamental compromise: either use high quality read alignments and experiment-specific models or sacrifice them for speed. We introduce Salmon, a quantification method that overcomes this restriction by combining a novel “lightweight” alignment procedure with a streaming parallel inference algorithm and a feature-rich model. These innovations yield both exceptional accuracy and order-of-magnitude speed benefits over traditional alignment-based methods.