Supported Applications


  • Description

    a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.

  • Installation

    Use the following command to install this title with the CLI client: $ biogrids-cli install kallisto Copy to clipboard
  • Primary Citation*

    N. L. Bray, H. Pimentel, and P. M. &. L. Pachter. 2016. Near-optimal probabilistic RNA-seq quantification. Nature Biotechnology. 34(5): 525-527.

    • *Full citation information available through

  • Webinars

    A brief introduction to the theory and method underlying kallisto for transcript quantification of RNA-Seq data.

    This screencast is from our IIHG MiniCourse training series on bioinformatic methods for U Iowa researchers.

    Find IIHG on the web at:

    You can find me at:; @ChimentiMichael on Twitter.

  • Keywords


  • Default Versions

    Linux 64:  0.46.2
    OS X INTEL:  0.46.2

  • Other Versions

      Linux 64:

    • OS X INTEL:

  • Developers

    Lior Pachter, Nicolas L Bray, Páll Melsted