Near-optimal probabilistic RNA-seq quantification

NL Bray, H Pimentel, P Melsted, L Pachter - Nature biotechnology, 2016 - nature.com
Nature biotechnology, 2016nature.com
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.
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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