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classify-consensus-vsearch: VSEARCH consensus taxonomy classifier

Citations

[feature-classifier:classify-consensus-vsearch:RFN+16]Torbjørn Rognes, Tomáš Flouri, Ben Nichols, Christopher Quince, and Frédéric Mahé. Vsearch: a versatile open source tool for metagenomics. PeerJ, 4:e2584, 2016. doi:10.7717/peerj.2584.

Docstring:

Usage: qiime feature-classifier classify-consensus-vsearch
           [OPTIONS]

  Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
  alignment between query and reference_reads, then assigns consensus
  taxonomy to each query sequence from among maxaccepts top hits,
  min_consensus of which share that taxonomic assignment. Unlike classify-
  consensus-blast, this method searches the entire reference database before
  choosing the top N hits, not the first N hits.

Options:
  --i-query ARTIFACT PATH FeatureData[Sequence]
                                  Sequences to classify taxonomically.
                                  [required]
  --i-reference-reads ARTIFACT PATH FeatureData[Sequence]
                                  reference sequences.  [required]
  --i-reference-taxonomy ARTIFACT PATH FeatureData[Taxonomy]
                                  reference taxonomy labels.  [required]
  --p-maxaccepts INTEGER RANGE    Maximum number of hits to keep for each
                                  query. Set to 0 to keep all hits >
                                  perc_identity similarity. Must be in range
                                  [0, infinity].  [default: 10]
  --p-perc-identity FLOAT         Reject match if percent identity to query is
                                  lower. Must be in range [0.0, 1.0].
                                  [default: 0.8]
  --p-strand [both|plus]          Align against reference sequences in forward
                                  ("plus") or both directions ("both").
                                  [default: both]
  --p-min-consensus FLOAT         Minimum fraction of assignments must match
                                  top hit to be accepted as consensus
                                  assignment. Must be in range (0.5, 1.0].
                                  [default: 0.51]
  --p-unassignable-label TEXT     [default: Unassigned]
  --p-threads INTEGER             [default: 1]
  --o-classification ARTIFACT PATH FeatureData[Taxonomy]
                                  The resulting taxonomy classifications.
                                  [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.feature_classifier.methods import classify_consensus_vsearch

Docstring:

VSEARCH consensus taxonomy classifier

Assign taxonomy to query sequences using VSEARCH. Performs VSEARCH global
alignment between query and reference_reads, then assigns consensus
taxonomy to each query sequence from among maxaccepts top hits,
min_consensus of which share that taxonomic assignment. Unlike classify-
consensus-blast, this method searches the entire reference database before
choosing the top N hits, not the first N hits.

Parameters
----------
query : FeatureData[Sequence]
    Sequences to classify taxonomically.
reference_reads : FeatureData[Sequence]
    reference sequences.
reference_taxonomy : FeatureData[Taxonomy]
    reference taxonomy labels.
maxaccepts : Int % Range(0, None), optional
    Maximum number of hits to keep for each query. Set to 0 to keep all
    hits > perc_identity similarity. Must be in range [0, infinity].
perc_identity : Float % Range(0.0, 1.0, inclusive_end=True), optional
    Reject match if percent identity to query is lower. Must be in range
    [0.0, 1.0].
strand : Str % Choices({'both', 'plus'}), optional
    Align against reference sequences in forward ("plus") or both
    directions ("both").
min_consensus : Float % Range(0.5, 1.0, inclusive_start=False, inclusive_end=True), optional
    Minimum fraction of assignments must match top hit to be accepted as
    consensus assignment. Must be in range (0.5, 1.0].
unassignable_label : Str, optional
threads : Int, optional

Returns
-------
classification : FeatureData[Taxonomy]
    The resulting taxonomy classifications.