RT Journal Article
SR Electronic
T1 Accurate, fast, and model-aware transcript expression quantification with Salmon
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 021592
DO 10.1101/021592
A1 Rob Patro
A1 Geet Duggal
A1 Carl Kingsford
YR 2015
UL http://biorxiv.org/content/early/2015/10/03/021592.abstract
AB 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.