Fork me on GitHub

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.

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