PT  - JOURNAL ARTICLE
AU  - Rob Patro
AU  - Geet Duggal
AU  - Carl Kingsford
TI  - Salmon: Accurate, Versatile and Ultrafast Quantification from RNA-seq Data using Lightweight-Alignment
AID  - 10.1101/021592
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 021592
4099  - http://biorxiv.org/content/early/2015/06/27/021592.short
4100  - http://biorxiv.org/content/early/2015/06/27/021592.full
AB  - Transcript quantification is a central task in the analysis of RNA-seq data. Accurate computational methods for the quantification of transcript abundances are essential for downstream analysis. However, most existing approaches are much slower than is necessary for their degree of accuracy. We introduce Salmon, a novel method and software tool for transcript quantification that exhibits state-of-the-art accuracy while being significantly faster than most other tools. Salmon achieves this through the combined application of a two-phase inference procedure, a reduced data representation, and a novel lightweight read alignment algorithm. Salmon is written in C++11, and is available under the GPL v3 license as open-source software at https://combine-lab.github.io/salmon.