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uchime-ref: Reference-based chimera filtering with vsearch.ΒΆ

Docstring:

Usage: qiime vsearch uchime-ref [OPTIONS]

  Apply the vsearch uchime_ref method to identify chimeric feature
  sequences. The results of this method can be used to filter chimeric
  features from the corresponding feature table. For additional details,
  please refer to the vsearch documentation.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          The feature sequences to be chimera-checked.
                                                                    [required]
  --i-table ARTIFACT FeatureTable[Frequency]
                          Feature table (used for computing total feature
                          abundances).                              [required]
  --i-reference-sequences ARTIFACT FeatureData[Sequence]
                          The non-chimeric reference sequences.     [required]
Parameters:
  --p-dn NUMBER           No vote pseudo-count, corresponding to the
    Range(0.0, None)      parameter n in the chimera scoring function.
                                                                [default: 1.4]
  --p-mindiffs INTEGER    Minimum number of differences per segment.
    Range(1, None)                                                [default: 3]
  --p-mindiv NUMBER       Minimum divergence from closest parent.
    Range(0.0, None)                                            [default: 0.8]
  --p-minh PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Minimum score (h). Increasing this value tends to
                          reduce the number of false positives and to decrease
                          sensitivity.                         [default: 0.28]
  --p-xn NUMBER Range(1.0, None, inclusive_start=False)
                          No vote weight, corresponding to the parameter beta
                          in the scoring function.              [default: 8.0]
  --p-threads INTEGER Range(0, 256, inclusive_end=True)
                          The number of threads to use for computation.
                          Passing 0 will launch one thread per CPU core.
                                                                  [default: 1]
Outputs:
  --o-chimeras ARTIFACT FeatureData[Sequence]
                          The chimeric sequences.                   [required]
  --o-nonchimeras ARTIFACT FeatureData[Sequence]
                          The non-chimeric sequences.               [required]
  --o-stats ARTIFACT      Summary statistics from chimera checking.
    UchimeStats                                                     [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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.vsearch.methods import uchime_ref

Docstring:

Reference-based chimera filtering with vsearch.

Apply the vsearch uchime_ref method to identify chimeric feature sequences.
The results of this method can be used to filter chimeric features from the
corresponding feature table. For additional details, please refer to the
vsearch documentation.

Parameters
----------
sequences : FeatureData[Sequence]
    The feature sequences to be chimera-checked.
table : FeatureTable[Frequency]
    Feature table (used for computing total feature abundances).
reference_sequences : FeatureData[Sequence]
    The non-chimeric reference sequences.
dn : Float % Range(0.0, None), optional
    No vote pseudo-count, corresponding to the parameter n in the chimera
    scoring function.
mindiffs : Int % Range(1, None), optional
    Minimum number of differences per segment.
mindiv : Float % Range(0.0, None), optional
    Minimum divergence from closest parent.
minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Minimum score (h). Increasing this value tends to reduce the number of
    false positives and to decrease sensitivity.
xn : Float % Range(1.0, None, inclusive_start=False), optional
    No vote weight, corresponding to the parameter beta in the scoring
    function.
threads : Int % Range(0, 256, inclusive_end=True), optional
    The number of threads to use for computation. Passing 0 will launch one
    thread per CPU core.

Returns
-------
chimeras : FeatureData[Sequence]
    The chimeric sequences.
nonchimeras : FeatureData[Sequence]
    The non-chimeric sequences.
stats : UchimeStats
    Summary statistics from chimera checking.