Wednesday, May 13, 2015

Near-optimal RNA-Seq quantification

Nicolas L. Bray, Harold Pimentel, Páll Melsted, and Lior Pachter
(Link) pdf

[Blog note:  This paper represents a significant advance in RNA sequencing methodology.  The paper is beautifully written and accessible for someone not in the field of bioinformatics.  Lior is covering the paper on his blog.]


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.

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