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

Docstring:

Usage: qiime cutadapt trim-paired [OPTIONS]

  Search demultiplexed paired-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.

Options:
  --i-demultiplexed-sequences ARTIFACT PATH SampleData[PairedEndSequencesWithQuality]
                                  The paired-end sequences to be trimmed.
                                  [required]
  --p-cores INTEGER RANGE         Number of CPU cores to use.  [default: 1]
  --p-adapter-f MULTIPLE TEXT     Sequence of an adapter ligated to the 3'
                                  end. The adapter and any subsequent bases
                                  are trimmed. If a `$` is appended, the
                                  adapter is only found if it is at the end of
                                  the read. Search in forward read. If your
                                  sequence of interest is "framed" by a 5' and
                                  a 3' adapter, use this parameter to define a
                                  "linked" primer - see
                                  https://cutadapt.readthedocs.io for complete
                                  details.  [optional]
  --p-front-f MULTIPLE TEXT       Sequence of an adapter ligated to the 5'
                                  end. The adapter and any preceding bases are
                                  trimmed. Partial matches at the 5' end are
                                  allowed. If a `^` character is prepended,
                                  the adapter is only found if it is at the
                                  beginning of the read. Search in forward
                                  read.  [optional]
  --p-anywhere-f MULTIPLE TEXT    Sequence of an adapter that may be ligated
                                  to the 5' or 3' end. Both types of matches
                                  as described under `adapter` and `front` are
                                  allowed. If the first base of the read is
                                  part of the match, the behavior is as with
                                  `front`, otherwise as with `adapter`. This
                                  option is mostly for rescuing failed library
                                  preparations - do not use if you know which
                                  end your adapter was ligated to. Search in
                                  forward read.  [optional]
  --p-adapter-r MULTIPLE TEXT     Sequence of an adapter ligated to the 3'
                                  end. The adapter and any subsequent bases
                                  are trimmed. If a `$` is appended, the
                                  adapter is only found if it is at the end of
                                  the read. Search in reverse 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-r MULTIPLE TEXT       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. Search in reverse
                                  read.  [optional]
  --p-anywhere-r MULTIPLE TEXT    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. Search in
                                  reverse read.  [optional]
  --p-error-rate FLOAT            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 RANGE         Remove multiple occurrences of an adapter if
                                  it is repeated, up to `times` times.
                                  [default: 1]
  --p-overlap INTEGER RANGE       Require at least `overlap` bases of overlap
                                  between 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]
  --o-trimmed-sequences ARTIFACT PATH SampleData[PairedEndSequencesWithQuality]
                                  The resulting trimmed sequences.  [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.cutadapt.methods import trim_paired

Docstring:

Find and remove adapters in demultiplexed paired-end sequences.

Search demultiplexed paired-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[PairedEndSequencesWithQuality]
    The paired-end sequences to be trimmed.
cores : Int % Range(1, None), optional
    Number of CPU cores to use.
adapter_f : List[Str], optional
    Sequence of an adapter ligated to the 3' end. The adapter and any
    subsequent bases are trimmed. If a `$` is appended, the adapter is only
    found if it is at the end of the read. Search in forward read. If your
    sequence of interest is "framed" by a 5' and a 3' adapter, use this
    parameter to define a "linked" primer - see
    https://cutadapt.readthedocs.io for complete details.
front_f : List[Str], optional
    Sequence of an adapter ligated to the 5' end. The adapter and any
    preceding bases are trimmed. Partial matches at the 5' end are allowed.
    If a `^` character is prepended, the adapter is only found if it is at
    the beginning of the read. Search in forward read.
anywhere_f : List[Str], optional
    Sequence of an adapter that may be ligated to the 5' or 3' end. Both
    types of matches as described under `adapter` and `front` are allowed.
    If the first base of the read is part of the match, the behavior is as
    with `front`, otherwise as with `adapter`. This option is mostly for
    rescuing failed library preparations - do not use if you know which end
    your adapter was ligated to. Search in forward read.
adapter_r : List[Str], optional
    Sequence of an adapter ligated to the 3' end. The adapter and any
    subsequent bases are trimmed. If a `$` is appended, the adapter is only
    found if it is at the end of the read. Search in reverse 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_r : 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. Search in reverse read.
anywhere_r : 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. Search in reverse read.
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.

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