conda activate qiime2-2020.11
qiime cutadapt trim-paired --help
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 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]
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 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).
--examples Show usage examples and exit.
--citations Show citations and exit.
--help Show this message and exit.
qiime cutadapt trim-single --help
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).
--examples Show usage examples and exit.
--citations Show citations and exit.
--help Show this message and exit.
