blast: BLAST+ local alignment search.¶

Docstring:

Usage: qiime feature-classifier blast [OPTIONS]

  Search for top hits in a reference database via local alignment between the
  query sequences and reference database sequences using BLAST+. Returns a
  report of the top M hits for each query (where M=maxaccepts).

Inputs:
  --i-query ARTIFACT FeatureData[Sequence]
                          Query sequences.                          [required]
  --i-reference-reads ARTIFACT FeatureData[Sequence]
                          Reference sequences. Incompatible with blastdb.
                                                                    [optional]
  --i-blastdb ARTIFACT    BLAST indexed database. Incompatible with
    BLASTDB               reference-reads.                          [optional]
Parameters:
  --p-maxaccepts INTEGER  Maximum number of hits to keep for each query.
    Range(1, None)        BLAST will choose the first N hits in the reference
                          database that exceed perc-identity similarity to
                          query. NOTE: the database is not sorted by
                          similarity to query, so these are the first N hits
                          that pass the threshold, not necessarily the top N
                          hits.                                  [default: 10]
  --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Reject match if percent identity to query is lower.
                                                                [default: 0.8]
  --p-query-cov PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Reject match if query alignment coverage per
                          high-scoring pair is lower. Note: this uses blastn's
                          qcov_hsp_perc parameter, and may not behave
                          identically to the query-cov parameter used by
                          classify-consensus-vsearch.           [default: 0.8]
  --p-strand TEXT Choices('both', 'plus', 'minus')
                          Align against reference sequences in forward
                          ("plus"), reverse ("minus"), or both directions
                          ("both").                          [default: 'both']
  --p-evalue NUMBER       BLAST expectation value (E) threshold for saving
                          hits.                               [default: 0.001]
  --p-output-no-hits / --p-no-output-no-hits
                          Report both matching and non-matching queries.
                          WARNING: always use the default setting for this
                          option unless if you know what you are doing! If you
                          set this option to False, your sequences and feature
                          table will need to be filtered to exclude
                          unclassified sequences, otherwise you may run into
                          errors downstream from missing feature IDs. Set to
                          FALSE to mirror default BLAST search.
                                                               [default: True]
  --p-num-threads NTHREADS
                          Number of threads (CPUs) to use in the BLAST
                          search. Pass 0 to use all available CPUs.
                                                                  [default: 1]
Outputs:
  --o-search-results ARTIFACT
    FeatureData[BLAST6]   Top hits for each query.                  [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.