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join-pairs: Join paired-end reads.ΒΆ

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]
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).
  --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.

Returns
-------
joined_sequences : SampleData[JoinedSequencesWithQuality]
    The joined sequences.