extract-seq-segments: Use reference sequences to extract shorter matching sequence segments from longer sequences based on a user-defined ‘perc-identity’ value.¶

Docstring:

Usage: qiime rescript extract-seq-segments [OPTIONS]

  This action provides the ability to extract a region, or segment, of
  sequence without the need to specify primer pairs. This is very useful in
  cases when one or more of the primer sequences are not present within the
  target sequences, which prevents extraction of the (amplicon) region through
  primer-pair searching. Here, VSEARCH is used to extract these segments based
  on a reference pool of sequences that only span the region of interest.

Inputs:
  --i-input-sequences ARTIFACT FeatureData[Sequence]
                         Sequences from which matching shorter sequence
                         segments (regions) can be extracted from. Sequences
                         containing segments that match those from
                         'reference-segment-sequences' will have those
                         segments extracted and written to file.    [required]
  --i-reference-segment-sequences ARTIFACT FeatureData[Sequence]
                         Reference sequence segments that will be used to
                         search for and extract matching segments from
                         'input-sequences'.                         [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.                             [default: 0.7]
  --p-target-coverage PROPORTION Range(0, 1, inclusive_start=False,
    inclusive_end=True)  The minimum fraction of coverage that
                         'reference-segment-sequences' must have in order to
                         extract matching segments from 'input-sequences'.
                                                                [default: 0.9]
  --p-min-seq-len INTEGER
    Range(1, None)       Minimum length of sequence allowed for searching.
                         Any sequence less than this will be discarded. If not
                         set, default program settings will be used.
                                                                    [optional]
  --p-threads INTEGER    Number of computation threads to use (1 to 256). The
    Range(1, 256)        number of threads should be lesser or equal to the
                         number of available CPU cores.           [default: 1]
Outputs:
  --o-extracted-sequence-segments ARTIFACT FeatureData[Sequence]
                         Extracted sequence segments from 'input-sequences'
                         that succesfully aligned to
                         'reference-segment-sequences'.             [required]
  --o-unmatched-sequences ARTIFACT FeatureData[Sequence]
                         Sequences in 'input-sequences' that did not have
                         matching sequence segments within
                         'reference-segment-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.