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decontam-remove: Remove contaminantsΒΆ

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.