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. 2016 May;34(5):525-7.
doi: 10.1038/nbt.3519. Epub 2016 Apr 4.

Near-optimal probabilistic RNA-seq quantification

Nicolas L Bray  1 , Harold Pimentel  2 , Páll Melsted  3 , Lior Pachter  2   4   5
Affiliations

Near-optimal probabilistic RNA-seq quantification

Nicolas L Bray et al. Nat Biotechnol. 2016 May.

Erratum in

Abstract

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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References

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