Near-optimal probabilistic RNA-seq quantification

@article{Bray2016NearoptimalPR,
  title={Near-optimal probabilistic RNA-seq quantification},
  author={Nicolas L. Bray and Harold Pimentel and P{\'a}ll Melsted and Lior Pachter},
  journal={Nature Biotechnology},
  year={2016},
  volume={34},
  pages={525-527}
}
We present kallisto, an RNA-seq quantification program that is two orders of magnitude faster than previous approaches and achieves similar accuracy. Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases. We use kallisto to analyze 30 million unaligned paired-end RNA-seq reads in <10 min on a standard laptop computer. This removes a major computational bottleneck in RNA-seq analysis. 

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