Near-optimal probabilistic RNA-seq quantification - PubMed (original) (raw)
doi: 10.1038/nbt.3519. Epub 2016 Apr 4.
Affiliations
- PMID: 27043002
- DOI: 10.1038/nbt.3519
Near-optimal probabilistic RNA-seq quantification
Nicolas L Bray et al. Nat Biotechnol. 2016 May.
Erratum in
- Erratum: Near-optimal probabilistic RNA-seq quantification.
Bray NL, Pimentel H, Melsted P, Pachter L. Bray NL, et al. Nat Biotechnol. 2016 Aug 9;34(8):888. doi: 10.1038/nbt0816-888d. Nat Biotechnol. 2016. PMID: 27504780 No abstract available.
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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