Docstring:
Usage: qiime quality-control decontam-remove [OPTIONS]
This method removes contaminant sequences from an OTU or ASV table and
returns the amended table to the user
Inputs:
--i-decontam-scores ARTIFACT FeatureData[DecontamScore]
Output table from decontam identify [required]
--i-table ARTIFACT FeatureTable[Frequency]
ASV or OTU table which contaminate sequences will be
identified from [required]
Parameters:
--p-threshold NUMBER Select threshold cutoff for decontam algorithm scores
[default: 0.1]
Outputs:
--o-filtered-table ARTIFACT FeatureTable[Frequency]
The resulting feature table of scores once
contaminants are removed [required]
Miscellaneous:
--output-dir PATH Output unspecified results to a directory
--verbose / --quiet Display verbose output to stdout and/or stderr during
execution of this action. Or silence output if
execution is successful (silence is golden).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--help Show this message and exit.
Import:
from qiime2.plugins.quality_control.methods import decontam_remove
Docstring:
Removes contaminant
This method removes contaminant sequences from an OTU or ASV table and
returns the amended table to the user
Parameters
----------
decontam_scores : FeatureData[DecontamScore]
Output table from decontam identify
table : FeatureTable[Frequency]
ASV or OTU table which contaminate sequences will be identified from
threshold : Float, optional
Select threshold cutoff for decontam algorithm scores
Returns
-------
filtered_table : FeatureTable[Frequency]
The resulting feature table of scores once contaminants are removed
