---
Name: Kallisto
URL: http://pachterlab.github.io/kallisto/
Description: >
  kallisto is a program for quantifying abundances of transcripts from RNA-Seq data.
---

The Kallisto module parses logs generated by
[Kallisto](http://pachterlab.github.io/kallisto/),
a program for quantifying abundances of transcripts from RNA-Seq data, or more generally
of target sequences using high-throughput sequencing reads.

**Note** - MultiQC parses the standard out from Kallisto, _not_ any of its output files
(`abundance.h5`, `abundance.tsv`, and `run_info.json`). As such, you must capture the
Kallisto stdout to a file when running to use the MultiQC module.
