Article,
Near-optimal probabilistic RNA-seq quantification
Nat Biotechnol, 34 (5): 525-527 (May 2016)
DOI: 10.1038/nbt.3519
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.
