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trim-single: Find and remove adapters in demultiplexed single-end sequences.ΒΆ

Docstring:

Usage: qiime cutadapt trim-single [OPTIONS]

  Search demultiplexed single-end sequences for adapters and remove them.
  The parameter descriptions in this method are adapted from the official
  cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
  for complete details.

Inputs:
  --i-demultiplexed-sequences ARTIFACT SampleData[SequencesWithQuality]
                        The single-end sequences to be trimmed.     [required]
Parameters:
  --p-cores INTEGER     Number of CPU cores to use.
    Range(1, None)                                                [default: 1]
  --p-adapter TEXT...   Sequence of an adapter ligated to the 3' end. The
    List[Str]           adapter and any subsequent bases are trimmed. If a `$`
                        is appended, the adapter is only found if it is at the
                        end of the read. If your sequence of interest is
                        "framed" by a 5' and a 3' adapter, use this parameter
                        to define a "linked" primer - see
                        https://cutadapt.readthedocs.io for complete details.
                                                                    [optional]
  --p-front TEXT...     Sequence of an adapter ligated to the 5' end. The
    List[Str]           adapter and any preceding bases are trimmed. Partial
                        matches at the 5' end are allowed. If a `^` character
                        is prepended, the adapter is only found if it is at
                        the beginning of the read.                  [optional]
  --p-anywhere TEXT...  Sequence of an adapter that may be ligated to the 5'
    List[Str]           or 3' end. Both types of matches as described under
                        `adapter` and `front` are allowed. If the first base
                        of the read is part of the match, the behavior is as
                        with `front`, otherwise as with `adapter`. This option
                        is mostly for rescuing failed library preparations -
                        do not use if you know which end your adapter was
                        ligated to.                                 [optional]
  --p-error-rate PROPORTION Range(0, 1, inclusive_end=True)
                        Maximum allowed error rate.             [default: 0.1]
  --p-indels / --p-no-indels
                        Allow insertions or deletions of bases when matching
                        adapters.                              [default: True]
  --p-times INTEGER     Remove multiple occurrences of an adapter if it is
    Range(1, None)      repeated, up to `times` times.            [default: 1]
  --p-overlap INTEGER   Require at least `overlap` bases of overlap between
    Range(1, None)      read and adapter for an adapter to be found.
                                                                  [default: 3]
  --p-match-read-wildcards / --p-no-match-read-wildcards
                        Interpret IUPAC wildcards (e.g., N) in reads.
                                                              [default: False]
  --p-match-adapter-wildcards / --p-no-match-adapter-wildcards
                        Interpret IUPAC wildcards (e.g., N) in adapters.
                                                               [default: True]
  --p-minimum-length INTEGER
    Range(1, None)      Discard reads shorter than specified value. Note, the
                        cutadapt default of 0 has been overridden, because
                        that value produces empty sequence records.
                                                                  [default: 1]
  --p-discard-untrimmed / --p-no-discard-untrimmed
                        Discard reads in which no adapter was found.
                                                              [default: False]
Outputs:
  --o-trimmed-sequences ARTIFACT SampleData[SequencesWithQuality]
                        The resulting trimmed 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).
  --citations           Show citations and exit.
  --help                Show this message and exit.

Import:

from qiime2.plugins.cutadapt.methods import trim_single

Docstring:

Find and remove adapters in demultiplexed single-end sequences.

Search demultiplexed single-end sequences for adapters and remove them. The
parameter descriptions in this method are adapted from the official
cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
for complete details.

Parameters
----------
demultiplexed_sequences : SampleData[SequencesWithQuality]
    The single-end sequences to be trimmed.
cores : Int % Range(1, None), optional
    Number of CPU cores to use.
adapter : List[Str], optional
    Sequence of an adapter ligated to the 3' end. The adapter and any
    subsequent bases are trimmed. If a `$` is appended, the adapter is only
    found if it is at the end of the read. If your sequence of interest is
    "framed" by a 5' and a 3' adapter, use this parameter to define a
    "linked" primer - see https://cutadapt.readthedocs.io for complete
    details.
front : List[Str], optional
    Sequence of an adapter ligated to the 5' end. The adapter and any
    preceding bases are trimmed. Partial matches at the 5' end are allowed.
    If a `^` character is prepended, the adapter is only found if it is at
    the beginning of the read.
anywhere : List[Str], optional
    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
    types of matches as described under `adapter` and `front` are allowed.
    If the first base of the read is part of the match, the behavior is as
    with `front`, otherwise as with `adapter`. This option is mostly for
    rescuing failed library preparations - do not use if you know which end
    your adapter was ligated to.
error_rate : Float % Range(0, 1, inclusive_end=True), optional
    Maximum allowed error rate.
indels : Bool, optional
    Allow insertions or deletions of bases when matching adapters.
times : Int % Range(1, None), optional
    Remove multiple occurrences of an adapter if it is repeated, up to
    `times` times.
overlap : Int % Range(1, None), optional
    Require at least `overlap` bases of overlap between read and adapter
    for an adapter to be found.
match_read_wildcards : Bool, optional
    Interpret IUPAC wildcards (e.g., N) in reads.
match_adapter_wildcards : Bool, optional
    Interpret IUPAC wildcards (e.g., N) in adapters.
minimum_length : Int % Range(1, None), optional
    Discard reads shorter than specified value. Note, the cutadapt default
    of 0 has been overridden, because that value produces empty sequence
    records.
discard_untrimmed : Bool, optional
    Discard reads in which no adapter was found.

Returns
-------
trimmed_sequences : SampleData[SequencesWithQuality]
    The resulting trimmed sequences.