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.