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decontam-remove: Remove contaminants¶
Docstring:
Usage: qiime quality-control decontam-remove [OPTIONS]
Remove contaminant sequences from a feature table and the associated
representative sequences.
Inputs:
--i-decontam-scores ARTIFACT FeatureData[DecontamScore]
Pre-feature decontam scores. [required]
--i-table ARTIFACT FeatureTable[Frequency]
Feature table from which contaminants will be
removed. [required]
--i-rep-seqs ARTIFACT FeatureData[Sequence]
Feature representative sequences from which
contaminants will be removed. [required]
Parameters:
--p-threshold PROPORTION Range(0.0, 1.0, inclusive_end=True)
Decontam score threshold. Features with a score less
than or equal to this threshold will be removed.
[default: 0.1]
Outputs:
--o-filtered-table ARTIFACT FeatureTable[Frequency]
Feature table with contaminants removed. [required]
--o-filtered-rep-seqs ARTIFACT FeatureData[Sequence]
Feature representative sequences with contaminants
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.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible to
all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.quality_control.methods import decontam_remove
Docstring:
Remove contaminants
Remove contaminant sequences from a feature table and the associated
representative sequences.
Parameters
----------
decontam_scores : FeatureData[DecontamScore]
Pre-feature decontam scores.
table : FeatureTable[Frequency]
Feature table from which contaminants will be removed.
rep_seqs : FeatureData[Sequence]
Feature representative sequences from which contaminants will be
removed.
threshold : Float % Range(0.0, 1.0, inclusive_end=True), optional
Decontam score threshold. Features with a score less than or equal to
this threshold will be removed.
Returns
-------
filtered_table : FeatureTable[Frequency]
Feature table with contaminants removed.
filtered_rep_seqs : FeatureData[Sequence]
Feature representative sequences with contaminants removed.