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.
InstallationUse the following command to install this title with the CLI client:
$ biogrids-cli install kallistoAvailable operating systems: Linux 64, OS X INTEL
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
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: http://www.michaelchimenti.com; @ChimentiMichael on Twitter.
Linux 64:  0.46.2 (25.1 MB)
OS X INTEL:  0.46.2 (10.5 MB)
Linux 64:0.43.1 (16.6 MB)
OS X INTEL:0.43.1 (2.6 MB)
Lior Pachter, Nicolas L Bray, Páll Melsted