merge-pairs: Merge paired-end reads.¶

Docstring:

Usage: qiime vsearch merge-pairs [OPTIONS]

  Merge paired-end sequence reads using vsearch's merge_pairs function. See
  the vsearch documentation for details on how paired-end merging 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 merged.
                                                                    [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 merging of staggered read pairs.
                                                              [default: False]
  --p-minovlen INTEGER   Minimum length of the area of overlap between reads
    Range(5, None)       during merging.                         [default: 10]
  --p-maxdiffs INTEGER   Maximum number of mismatches in the area of overlap
    Range(0, None)       during merging.                         [default: 10]
  --p-minmergelen INTEGER
    Range(0, None)       Minimum length of the merged read to be retained.
                                                                    [optional]
  --p-maxmergelen INTEGER
    Range(0, None)       Maximum length of the merged read to be retained.
                                                                    [optional]
  --p-maxee NUMBER       Maximum number of expected errors in the merged read
    Range(0.0, None)     to be retained.                            [optional]
  --p-threads NTHREADS   The number of threads to use for computation. Does
                         not scale much past 4 threads.           [default: 1]
Outputs:
  --o-merged-sequences ARTIFACT SampleData[JoinedSequencesWithQuality]
                         The merged sequences.                      [required]
  --o-unmerged-sequences ARTIFACT SampleData[PairedEndSequencesWithQuality]
                         The unmerged paired-end reads.             [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.