Usage: qiime cutadapt trim-paired [OPTIONS]Search demultiplexed paired-end sequences for adapters and remove them.
搜索并删除双末端序列中得接头序列
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 INTEGERNumber 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]
连接到3’端得接头，裁剪接头序列和其后任意碱基。如果附加了' $ '，则只有在read的末尾才会检索接头。向前检索。
--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]
连接到5'端接头的序列。裁剪接头和前面任意碱基。允许5'端部分匹配。如果添加了' ^ '字符，则只有在read开始时才检索接头。
--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 INTEGERRemove multiple occurrences of an adapter if it is
Range(1, None)repeated, up to `times` times.[default: 1]
--p-overlap INTEGERRequire 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 PATHOutput unspecified results to a directory
--verbose / --quietDisplay verbose output to stdout and/or stderr
during execution of this action. Or silence output
if execution is successful (silence is golden).
--examplesShow usage examples and exit.
--citationsShow citations and exit.
--helpShow this message and exit.
