TY - JOUR T1 - Accurate, fast, and model-aware transcript expression quantification with Salmon JF - bioRxiv DO - 10.1101/021592 SP - 021592 AU - Rob Patro AU - Geet Duggal AU - Carl Kingsford Y1 - 2015/01/01 UR - http://biorxiv.org/content/early/2015/10/03/021592.abstract N2 - 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 bias model. These innovations yield both exceptional accuracy and order-of-magnitude speed benefits over traditional alignment-based methods. ER -