Near-optimal RNA-Seq quantification

Nicolas L. Bray, Harold Pimentel, Páll Melsted and Lior Pachter*, 1. Innovative Genomics Initiative, UC Berkeley 2. Department of Computer Science, UC Berkeley 3. Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland 4. Departments of Mathematics and Molecular & Cell Biology, UC Berkeley * Corresponding author: [email protected] 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 paired-end 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.