exclude-seqs: Exclude sequences by alignment¶

Docstring:

Usage: qiime quality-control exclude-seqs [OPTIONS]

  This method aligns feature sequences to a set of reference sequences to
  identify sequences that hit/miss the reference within a specified
  perc_identity, evalue, and perc_query_aligned. This method could be used to
  define a positive filter, e.g., extract only feature sequences that align to
  a certain clade of bacteria; or to define a negative filter, e.g., identify
  sequences that align to contaminant or human DNA sequences that should be
  excluded from subsequent analyses. Note that filtering is performed based on
  the perc_identity, perc_query_aligned, and evalue thresholds (the latter
  only if method==BLAST and an evalue is set). Set perc_identity==0 and/or
  perc_query_aligned==0 to disable these filtering thresholds as necessary.

Inputs:
  --i-query-sequences ARTIFACT FeatureData[Sequence]
                          Sequences to test for exclusion           [required]
  --i-reference-sequences ARTIFACT FeatureData[Sequence]
                          Reference sequences to align against feature
                          sequences                                 [required]
Parameters:
  --p-method VALUE Str % Choices('blast', 'blastn-short')¹ | Str %
    Choices('vsearch')²   Alignment method to use for matching feature
                          sequences against reference sequences
                                                            [default: 'blast']
  --p-perc-identity PROPORTION Range(0.0, 1.0, inclusive_end=True)
                          Reject match if percent identity to reference is
                          lower. Must be in range [0.0, 1.0]   [default: 0.97]
  --p-evalue NUMBER       BLAST expectation (E) value threshold for saving
                          hits. Reject if E value is higher than threshold.
                          This threshold is disabled by default.    [optional]
  --p-perc-query-aligned NUMBER
                          Percent of query sequence that must align to
                          reference in order to be accepted as a hit.
                                                               [default: 0.97]
  --p-threads NTHREADS    Number of threads to use. Only applies to vsearch
                          method.                                 [default: 1]
  --p-left-justify VALUE Bool % Choices(False)¹ | Bool²
                          Reject match if the pairwise alignment begins with
                          gaps                                [default: False]
Outputs:
  --o-sequence-hits ARTIFACT FeatureData[Sequence]
                          Subset of feature sequences that align to reference
                          sequences                                 [required]
  --o-sequence-misses ARTIFACT FeatureData[Sequence]
                          Subset of feature sequences that do not align to
                          reference sequences                       [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.