Nature Journals Nature Biotechnology Bray, N., Pimentel, H., Melsted, P., Pachter, L.: Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology Vol. 34, pages 525–527, 2016 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