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QIIME2LEFSE(1) User Commands QIIME2LEFSE(1)

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:

show this help message and exit
the Qiime OTU table file [ stdin if not present ]
the Qiime OTU table file [ only OTU table without metadata if not present ]
the output file [stdout if not present]
the attribute to use as class
the attribute to use as subclass
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.

September 2019 qiime2lefse 1.0.8