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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.

Options:
  --i-demultiplexed-seqs ARTIFACT PATH SampleData[PairedEndSequencesWithQuality]
                                  The demultiplexed paired-end sequences to be
                                  joined.  [required]
  --p-truncqual INTEGER RANGE     Truncate sequences at the first base with
                                  the specified quality score value or lower.
                                  [optional]
  --p-minlen INTEGER RANGE        Sequences shorter than minlen after
                                  truncation are discarded.  [default: 1]
  --p-maxns INTEGER RANGE         Sequences with more than maxns N characters
                                  are discarded.  [optional]
  --p-allowmergestagger / --p-no-allowmergestagger
                                  Allow joining of staggered read pairs.
                                  [default: False]
  --p-minovlen INTEGER RANGE      Minimum overlap length of forward and
                                  reverse reads for joining.  [default: 10]
  --p-maxdiffs INTEGER RANGE      Maximum number of mismatches in the
                                  forward/reverse read overlap for joining.
                                  [default: 10]
  --p-minmergelen INTEGER RANGE   Minimum length of the joined read to be
                                  retained.  [optional]
  --p-maxmergelen INTEGER RANGE   Maximum length of the joined read to be
                                  retained.  [optional]
  --p-maxee FLOAT                 Maximum number of expected errors in the
                                  joined read to be retained.  [optional]
  --p-qmin INTEGER RANGE          The minimum allowed quality score in the
                                  input.  [default: 0]
  --p-qminout INTEGER RANGE       The minimum allowed quality score to use in
                                  output.  [default: 0]
  --p-qmax INTEGER RANGE          The maximum allowed quality score in the
                                  input.  [default: 41]
  --p-qmaxout INTEGER RANGE       The maximum allowed quality score to use in
                                  output.  [default: 41]
  --o-joined-sequences ARTIFACT PATH SampleData[JoinedSequencesWithQuality]
                                  The joined sequences.  [required if not
                                  passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --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.