Near optimal probabilistic RNA seq quantification
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.
Nature Biotechnology