title: Near-optimal probabilistic RNA-seq quantification.
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.
authors.affiliation: Innovative Genomics Initiative, University of California, Berkeley, California, USA.
authors.forename: Nicolas L
authors.initials: NL
authors.lastname: Bray
authors.affiliation: Department of Computer Science, University of California, Berkeley, California, USA.
authors.forename: Harold
authors.initials: H
authors.lastname: Pimentel
authors.affiliation: Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, University of Iceland, Reykjavik, Iceland.
authors.forename: Páll
authors.identifier: 0000-0002-8418-6724
authors.initials: P
authors.lastname: Melsted
authors.affiliation: 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.
authors.forename: Lior
authors.initials: L
authors.lastname: Pachter
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D015233:Models, Statistical; D010363:Pattern Recognition, Automated / Q000379:methods; D012313:RNA / Q000235:genetics*; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity; D016415:Sequence Alignment / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods*; D012984:Software
chemical_list: D012313:RNA