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.Comment: - Added some results (paralog analysis, allele specific expression
analysis, alignment comparison, accuracy analysis with TPMs) - Switched
bootstrap analysis to human sample from SEQC-MAQCIII - Provided link to a
snakefile that allows for reproducibility of all results and figures in the
pape
