Docstring:
Usage: qiime vsearch join-pairs [OPTIONS]
Join paired-end sequence reads using vsearch's merge_pairs function. The
qmin, qminout, qmax, and qmaxout parameters should only need to be
modified when working with older fastq sequence data. See the vsearch
documentation for details on how paired-end joining is performed, and for
more information on the parameters to this method.
Inputs:
--i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
The demultiplexed paired-end sequences to be joined.
[required]
Parameters:
--p-truncqual INTEGER Truncate sequences at the first base with the
Range(0, None) specified quality score value or lower. [optional]
--p-minlen INTEGER Sequences shorter than minlen after truncation are
Range(0, None) discarded. [default: 1]
--p-maxns INTEGER Sequences with more than maxns N characters are
Range(0, None) discarded. [optional]
--p-allowmergestagger / --p-no-allowmergestagger
Allow joining of staggered read pairs.
[default: False]
--p-minovlen INTEGER Minimum overlap length of forward and reverse reads
Range(0, None) for joining. [default: 10]
--p-maxdiffs INTEGER Maximum number of mismatches in the forward/reverse
Range(0, None) read overlap for joining. [default: 10]
--p-minmergelen INTEGER
Range(0, None) Minimum length of the joined read to be retained.
[optional]
--p-maxmergelen INTEGER
Range(0, None) Maximum length of the joined read to be retained.
[optional]
--p-maxee NUMBER Maximum number of expected errors in the joined read
Range(0.0, None) to be retained. [optional]
--p-qmin INTEGER Range(-5, 2, inclusive_end=True)
The minimum allowed quality score in the input.
[default: 0]
--p-qminout INTEGER Range(-5, 2, inclusive_end=True)
The minimum allowed quality score to use in output.
[default: 0]
--p-qmax INTEGER Range(40, 41, inclusive_end=True)
The maximum allowed quality score in the input.
[default: 41]
--p-qmaxout INTEGER Range(40, 41, inclusive_end=True)
The maximum allowed quality score to use in output.
[default: 41]
--p-threads INTEGER Range(0, 8, inclusive_end=True)
The number of threads to use for computation. Does
not scale much past 4 threads. [default: 1]
Outputs:
--o-joined-sequences ARTIFACT SampleData[JoinedSequencesWithQuality]
The joined 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.
Import:
from qiime2.plugins.vsearch.methods import join_pairs
Docstring:
Join paired-end reads.
Join paired-end sequence reads using vsearch's merge_pairs function. The
qmin, qminout, qmax, and qmaxout parameters should only need to be modified
when working with older fastq sequence data. See the vsearch documentation
for details on how paired-end joining is performed, and for more
information on the parameters to this method.
Parameters
----------
demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
The demultiplexed paired-end sequences to be joined.
truncqual : Int % Range(0, None), optional
Truncate sequences at the first base with the specified quality score
value or lower.
minlen : Int % Range(0, None), optional
Sequences shorter than minlen after truncation are discarded.
maxns : Int % Range(0, None), optional
Sequences with more than maxns N characters are discarded.
allowmergestagger : Bool, optional
Allow joining of staggered read pairs.
minovlen : Int % Range(0, None), optional
Minimum overlap length of forward and reverse reads for joining.
maxdiffs : Int % Range(0, None), optional
Maximum number of mismatches in the forward/reverse read overlap for
joining.
minmergelen : Int % Range(0, None), optional
Minimum length of the joined read to be retained.
maxmergelen : Int % Range(0, None), optional
Maximum length of the joined read to be retained.
maxee : Float % Range(0.0, None), optional
Maximum number of expected errors in the joined read to be retained.
qmin : Int % Range(-5, 2, inclusive_end=True), optional
The minimum allowed quality score in the input.
qminout : Int % Range(-5, 2, inclusive_end=True), optional
The minimum allowed quality score to use in output.
qmax : Int % Range(40, 41, inclusive_end=True), optional
The maximum allowed quality score in the input.
qmaxout : Int % Range(40, 41, inclusive_end=True), optional
The maximum allowed quality score to use in output.
threads : Int % Range(0, 8, inclusive_end=True), optional
The number of threads to use for computation. Does not scale much past
4 threads.
Returns
-------
joined_sequences : SampleData[JoinedSequencesWithQuality]
The joined sequences.
