Near-optimal RNA-Seq quantification
Nicolas Bray, Harold Pimentel, Páll Melsted, Lior Pachter
Subjects: Quantitative Methods (q-bio.QM); Computational Engineering, Finance, and Science (cs.CE); Data Structures and Algorithms (cs.DS); Genomics (q-bio.GN)

We present a novel approach to RNA-Seq quantification that is near optimal in speed and accuracy. Software implementing the approach, called kallisto, can be used to analyze 30 million unaligned RNA-Seq reads in less than 5 minutes on a standard laptop computer while providing results as accurate as those of the best existing tools. This removes a major computational bottleneck in RNA-Seq analysis.