qiime cutadapt trim-paired (version 2019.4)

--i-demultiplexed-sequences: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end sequences to be trimmed. [required]:

--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-no-indels: Do not allow insertions or deletions of bases when matching adapters. [default: False]:

--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-no-match-adapter-wildcards: Do not interpret IUPAC wildcards (e.g., N) in adapters. [default: False]:

--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]:

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.
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.