NAME

       qiime2lefse.py - determine features of organisms, clades, taxonomic units, genes

DESCRIPTION

       usage: qiime2lefse.py [-h] [--in [INPUT_FILE]] [--md [METADATA_FILE]]

       [--out [OUTPUT_FILE]] [-c class attribute]
              [-s subclass attribute] [-u subject attribute]

       Script  will  convert  QIIME TSV BIOM table for use with lefse. It is imperative that this table has taxa
       metadata associated with it named 'Consensus Lineage', this can be down with e.g. the follow biom convert
       script: ---- biom convert -i otu.biom  -o  otu.txt  --to-tsv  --header-key  Taxonomy  --outputmetadata-id
       'Consensus Lineage'

   optional arguments:
       -h, --help
              show this help message and exit

       --in [INPUT_FILE]
              the Qiime OTU table file [ stdin if not present ]

       --md [METADATA_FILE]
              the Qiime OTU table file [ only OTU table without metadata if not present ]

       --out [OUTPUT_FILE]
              the output file [stdout if not present]

       -c class attribute
              the attribute to use as class

       -s subclass attribute
              the attribute to use as subclass

       -u subject attribute
              the attribute to use as subject

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.

qiime2lefse.py 1.1.2                             September 2021                                QIIME2LEFSE.PY(1)