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output.md

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Outputs

The pipeline generates the following outputs depending on which modules were activated, located under "results", if no custom --outdir was set.

  • MultiQCA folder that contains the combined QC reports
  • pipeline_info A folder containing workflow traces and a file containing all software versions used in the performed workflow.
  • humann A folder that contains the merged result tables of HUMAnN3
  • Metaphlan4 A folder containing the merged abundances tables of Metaphlan4
  • Kraken A folder containing the merged abundances tables of Kraken
  • sylth A folder containing the abundances profiles calculated with sylth
  • salmon A folder containing the abundances profiles calculated with salmon
  • FastQC A folder containing all FASTQC outputs as zip and html Assembly outputs:
  • checkm A folder containing all checkm outputs
  • GTDBTK A folder containing all GTDB-TK outputs
  • MAG_abundance A folder containing all estimated MAG abundances per sample
  • magscot A folder containing all magscot outputs
  • counttable A folder containing count tables for created contigs per sample