Kallisto

Inroducion

It's the new (2015) way of evaluating gene expression abundance from NGS short reads.

It is considerably faster than other methods (like those based on say, RSEM) in that it omits the conventional alignment step, and instead calculates what it calls compatibility classes for each read, which are transcripts that the read could align with, if a proper alignment had taken place.

Steps in Brief

First off, we need an assembly of some sort: a reference transcriptome or genome, which may have been de-novo assembled. AS is often the case, this needs to be indexed first. Kallisto has its own tool for that:

kallisto index -i transcripts.idx transcripts.fasta.gz

Links

• Kallisto's own getting started page at starting
• benchtobioinformatics
• Andrew MacKenzie

Analysis

Also part of Lior Pachter's lab is the Sleuth software and this is recommended for analysis of kallisto output