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, 34 (5), 525-7

Near-optimal Probabilistic RNA-seq Quantification


Near-optimal Probabilistic RNA-seq Quantification

Nicolas L Bray et al. Nat Biotechnol.

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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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