Patro, RobDuggal, GeetLove, Michael IIrizarry, RafaelKingsford, Carl2017-12-052017Patro, Rob, Geet Duggal, Michael I Love, Rafael A Irizarry, and Carl Kingsford. 2017. “Salmon: fast and bias-aware quantification of transcript expression using dual-phase inference.” Nature methods 14 (4): 417-419. doi:10.1038/nmeth.4197. http://dx.doi.org/10.1038/nmeth.4197.http://nrs.harvard.edu/urn-3:HUL.InstRepos:34491813We introduce Salmon, a method for quantifying transcript abundance from RNA-seq reads that is accurate and fast. Salmon is the first transcriptome-wide quantifier to correct for fragment GC content bias, which we demonstrate substantially improves the accuracy of abundance estimates and the reliability of subsequent differential expression analysis. Salmon combines a new dual-phase parallel inference algorithm and feature-rich bias models with an ultra-fast read mapping procedure.en-USJournal Article2017-12-0510.1038/nmeth.4197