Near-optimal Probabilistic RNA-seq Quantification

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

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

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*

Substances

  • RNA