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PMID: 27043002 Published · ppublish English Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Near-optimal probabilistic RNA-seq quantification.

Nature biotechnology ·Vol. 34 ·No. 5 ·2016-00-00 ·Pages 525-7

Bray NL, Pimentel H, Melsted P, Pachter L

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.

MeSH Terms
Algorithms Computer Simulation Data Interpretation, Statistical High-Throughput Nucleotide Sequencing/methods Models, Statistical Pattern Recognition, Automated/methods RNA/genetics Reproducibility of Results Sensitivity and Specificity Sequence Alignment/methods Sequence Analysis, RNA/methods Software
Chemicals
RNA
Authors & Affiliations
4 authors, click to expand affiliations / ORCID
Bray Nicolas L
Innovative Genomics Initiative, University of California, Berkeley, California, USA.
Pimentel Harold
Department of Computer Science, University of California, Berkeley, California, USA.
Melsted Páll ORCID
Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
Pachter Lior
Department of Computer Science, University of California, Berkeley, California, USA. | Department of Mathematics, University of California, Berkeley, California, USA. | Department of Molecular &Cell Biology, University of California, Berkeley, California, USA.
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Article Info
Journal
Nature biotechnology
Abbr.
Nat Biotechnol
ISSN
1546-1696
DOI
10.1038/nbt.3519
Published
2016-00-00
Epub
2016-00-04
Pages
525-7
Language
English
Region
United States
NLM ID
9604648
Subset
IM
Grants
NHGRI NIH HHS · R01 HG006129 · United States
Corrections
ErratumIn
PMID: 27504780
External Links
PubMed source DOI: 10.1038/nbt.3519 View journal details
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