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Kallisto

Quantifies abundances of transcripts (or more generally, of target sequences) from RNA-Seq data

http://pachterlab.github.io/kallisto/

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.

File search patterns​

kallisto:
  contents: "[quant] finding pseudoalignments for the reads"