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dereplicate-sequences: Dereplicate sequences.ΒΆ

Docstring:

Usage: qiime vsearch dereplicate-sequences [OPTIONS]

  Dereplicate sequence data and create a feature table and feature
  representative sequences. Feature identifiers in the resulting artifacts
  will be the sha1 hash of the sequence defining each feature. If clustering
  of features into OTUs is desired, the resulting artifacts can be passed to
  the cluster_features_* methods in this plugin.

Options:
  --i-sequences ARTIFACT PATH SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences]
                                  The sequences to be dereplicated.
                                  [required]
  --p-derep-prefix / --p-no-derep-prefix
                                  Merge sequences with identical prefixes. If
                                  a sequence is identical to the prefix of two
                                  or more longer sequences, it is clustered
                                  with the shortest of them. If they are
                                  equally long, it is clustered with the most
                                  abundant.  [default: False]
  --o-dereplicated-table ARTIFACT PATH FeatureTable[Frequency]
                                  The table of dereplicated sequences.
                                  [required if not passing --output-dir]
  --o-dereplicated-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The dereplicated sequences.  [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 dereplicate_sequences

Docstring:

Dereplicate sequences.

Dereplicate sequence data and create a feature table and feature
representative sequences. Feature identifiers in the resulting artifacts
will be the sha1 hash of the sequence defining each feature. If clustering
of features into OTUs is desired, the resulting artifacts can be passed to
the cluster_features_* methods in this plugin.

Parameters
----------
sequences : SampleData[JoinedSequencesWithQuality] | SampleData[SequencesWithQuality] | SampleData[Sequences]
    The sequences to be dereplicated.
derep_prefix : Bool, optional
    Merge sequences with identical prefixes. If a sequence is identical to
    the prefix of two or more longer sequences, it is clustered with the
    shortest of them. If they are equally long, it is clustered with the
    most abundant.

Returns
-------
dereplicated_table : FeatureTable[Frequency]
    The table of dereplicated sequences.
dereplicated_sequences : FeatureData[Sequence]
    The dereplicated sequences.