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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.

Options:
  --i-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The feature sequences to be chimera-checked.
                                  [required]
  --i-table ARTIFACT PATH FeatureTable[Frequency]
                                  Feature table (used for computing total
                                  feature abundances).  [required]
  --i-reference-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The non-chimeric reference sequences.
                                  [required]
  --p-dn FLOAT                    No vote pseudo-count, corresponding to the
                                  parameter n in the chimera scoring function.
                                  [default: 1.4]
  --p-mindiffs INTEGER RANGE      Minimum number of differences per segment.
                                  [default: 3]
  --p-mindiv FLOAT                Minimum divergence from closest parent.
                                  [default: 0.8]
  --p-minh FLOAT                  Minimum score (h). Increasing this value
                                  tends to reduce the number of false
                                  positives and to decrease sensitivity.
                                  [default: 0.28]
  --p-xn FLOAT                    No vote weight, corresponding to the
                                  parameter beta in the scoring function.
                                  [default: 8.0]
  --p-threads INTEGER RANGE       The number of threads to use for
                                  computation. Passing 0 will launch one
                                  thread per CPU core.  [default: 1]
  --o-chimeras ARTIFACT PATH FeatureData[Sequence]
                                  The chimeric sequences.  [required if not
                                  passing --output-dir]
  --o-nonchimeras ARTIFACT PATH FeatureData[Sequence]
                                  The non-chimeric sequences.  [required if
                                  not passing --output-dir]
  --o-stats ARTIFACT PATH UchimeStats
                                  Summary statistics from chimera checking.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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.