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 NTHREADS Number of CPU cores to use. [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]
--p-max-expected-errors NUMBER
Range(0, None) Discard reads that exceed maximum expected
erroneous nucleotides. [optional]
--p-max-n NUMBER Discard reads with more than COUNT N bases. If
Range(0, None) COUNT_or_FRACTION is a number between 0 and 1, it is
interpreted as a fraction of the read length.
[optional]
--p-quality-cutoff-5end INTEGER
Range(0, None) Trim nucleotides with Phred score quality lower
than threshold from 5 prime end. [default: 0]
--p-quality-cutoff-3end INTEGER
Range(0, None) Trim nucleotides with Phred score quality lower
than threshold from 3 prime end. [default: 0]
--p-quality-base INTEGER
Range(0, None) How the Phred score is encoded (33 or 64).
[default: 33]
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).
--example-data PATH Write example data and exit.
--citations Show citations and exit.
--use-cache DIRECTORY Specify the cache to be used for the intermediate
work of this action. If not provided, the default
cache under $TMP/qiime2/ will be used.
IMPORTANT FOR HPC USERS: If you are on an HPC system
and are using parallel execution it is important to
set this to a location that is globally accessible
to all nodes in the cluster.
--help Show this message and exit.
Import:
from qiime2.plugins.cutadapt.methods import trim_paired
Docstring:
Find and remove adapters in demultiplexed paired-end sequences.
Search demultiplexed paired-end sequences for adapters and remove them. The
parameter descriptions in this method are adapted from the official
cutadapt docs - please see those docs at https://cutadapt.readthedocs.io
for complete details.
Parameters
----------
demultiplexed_sequences : SampleData[PairedEndSequencesWithQuality]
The paired-end sequences to be trimmed.
cores : Threads, optional
Number of CPU cores to use.
adapter_f : List[Str], optional
Sequence of an adapter ligated to the 3' end. The adapter and any
subsequent bases are trimmed. If a `$` 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.
max_expected_errors : Float % Range(0, None), optional
Discard reads that exceed maximum expected erroneous nucleotides.
max_n : Float % Range(0, None), optional
Discard reads with more than COUNT N bases. If COUNT_or_FRACTION is a
number between 0 and 1, it is interpreted as a fraction of the read
length.
quality_cutoff_5end : Int % Range(0, None), optional
Trim nucleotides with Phred score quality lower than threshold from 5
prime end.
quality_cutoff_3end : Int % Range(0, None), optional
Trim nucleotides with Phred score quality lower than threshold from 3
prime end.
quality_base : Int % Range(0, None), optional
How the Phred score is encoded (33 or 64).
Returns
-------
trimmed_sequences : SampleData[PairedEndSequencesWithQuality]
The resulting trimmed sequences.
