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.
@article{arxiv.1505.02710,
title = {Near-optimal RNA-Seq quantification},
author = {Nicolas Bray and Harold Pimentel and Páll Melsted and Lior Pachter},
journal= {arXiv preprint arXiv:1505.02710},
year = {2015}
}
Comments
- 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 paper