Back

Kallisto

Kallisto

Description

kallisto is 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.

 


Available

Version on CSC's Servers


Taito: 0.44.0


Usage

To load the default version on Taito you can use

module load kallisto

For usage help use:

kallisto

For help on writing batch job scripts see the Taito User Guide.

Sleuth

sleuth is a program for differential analysis of RNA-Seq data. It makes use of quantification uncertainty estimates obtained via kallisto for accurate differential analysis of isoforms or genes, allows testing in the context of experiments with complex designs, and supports interactive exploratory data analysis via sleuth live.

To use sleuth:

module load r-env/3.5.1

To use sleuth and kallisto together, load the r-env module first:

module load r-env/3.5.1
module load kallisto


Discipline

Biosciences

References

Kallisto:

  1. Nicolas L Bray, Harold Pimentel, Páll Melsted and Lior Pachter, Near-optimal probabilistic RNA-seq quantification, Nature Biotechnology 34, 525–527 (2016), doi:10.1038/nbt.3519

Sleuth:

  1. H Pimentel, NL Bray, S Puente, P Melsted and Lior Pachter, Differential analysis of RNA-seq incorporating quantification uncertainty, Nature Methods 14, 687–690 (2017), doi:10.1038/nmeth.4324


Support

servicedesk@csc.fi


Manual