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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. 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-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).
  --example-data PATH    Write example data 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. 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.
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.