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Nat Biotechnol. 2016 May;34(5):525-7. doi: 10.1038/nbt.3519. Epub 2016 Apr 4.

Near-optimal probabilistic RNA-seq quantification.

Author information

1
Innovative Genomics Initiative, University of California, Berkeley, California, USA.
2
Department of Computer Science, University of California, Berkeley, California, USA.
3
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
4
Department of Mathematics, University of California, Berkeley, California, USA.
5
Department of Molecular &Cell Biology, University of California, Berkeley, California, USA.

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.

PMID:
27043002
DOI:
10.1038/nbt.3519
[Indexed for MEDLINE]

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