NAME

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

SYNOPSIS

       qiime2lefse  [-h]  [--in  [INPUT_FILE]]  [--md  [METADATA_FILE]] [--out [OUTPUT_FILE]] [-c
       class attribute] [-s subclass attribute] [-u subject attribute]

DESCRIPTION

       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'

OPTIONS

   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.