cluster-features-closed-reference: Closed-reference clustering of features.¶

Docstring:

Usage: qiime vsearch cluster-features-closed-reference [OPTIONS]

  Given a feature table and the associated feature sequences, cluster the
  features against a reference database based on user-specified percent
  identity threshold of their sequences. This is not a general-purpose closed-
  reference clustering method, but rather is intended to be used for
  clustering the results of quality-filtering/dereplication methods, such as
  DADA2, or for re-clustering a FeatureTable at a lower percent identity than
  it was originally clustered at. When a group of features in the input table
  are clustered into a single feature, the frequency of that single feature in
  a given sample is the sum of the frequencies of the features that were
  clustered in that sample. Feature identifiers will be inherited from the
  centroid feature of each cluster. See the vsearch documentation for details
  on how sequence clustering is performed.

Inputs:
  --i-sequences ARTIFACT FeatureData[Sequence]
                          The sequences corresponding to the features in
                          table.                                    [required]
  --i-table ARTIFACT FeatureTable[Frequency]
                          The feature table to be clustered.        [required]
  --i-reference-sequences ARTIFACT FeatureData[Sequence]
                          The sequences to use as cluster centroids.
                                                                    [required]
Parameters:
  --p-perc-identity PROPORTION Range(0, 1, inclusive_start=False,
    inclusive_end=True)   The percent identity at which clustering should be
                          performed. This parameter maps to vsearch's --id
                          parameter.                                [required]
  --p-strand TEXT Choices('plus', 'both')
                          Search plus (i.e., forward) or both (i.e., forward
                          and reverse complement) strands.   [default: 'plus']
  --p-threads NTHREADS    The number of threads to use for computation.
                          Passing 0 will launch one thread per CPU core.
                                                                  [default: 1]
Outputs:
  --o-clustered-table ARTIFACT FeatureTable[Frequency]
                          The table following clustering of features.
                                                                    [required]
  --o-clustered-sequences ARTIFACT FeatureData[Sequence]
                          The sequences representing clustered features,
                          relabeled by the reference IDs.           [required]
  --o-unmatched-sequences ARTIFACT FeatureData[Sequence]
                          The sequences which failed to match any reference
                          sequences. This output maps to vsearch's
                          --notmatched parameter.                   [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.