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emp-paired: Demultiplex paired-end sequence data generated with the EMP protocol.ΒΆ

Docstring:

Usage: qiime demux emp-paired [OPTIONS]

  Demultiplex paired-end sequence data (i.e., map barcode reads to sample
  ids) for data generated with the Earth Microbiome Project (EMP) amplicon
  sequencing protocol. Details about this protocol can be found at
  http://www.earthmicrobiome.org/protocols-and-standards/

Options:
  --i-seqs ARTIFACT PATH EMPPairedEndSequences
                                  The paired-end sequences to be
                                  demultiplexed.  [required]
  --m-barcodes-file MULTIPLE FILE
                                  Metadata file or artifact viewable as
                                  metadata. This option may be supplied
                                  multiple times to merge metadata.
                                  [required]
  --m-barcodes-column MetadataColumn[Categorical]
                                  Column from metadata file or artifact
                                  viewable as metadata. The sample metadata
                                  column containing the per-sample barcodes.
                                  [required]
  --p-rev-comp-barcodes / --p-no-rev-comp-barcodes
                                  If provided, the barcode sequence reads will
                                  be reverse complemented prior to
                                  demultiplexing.  [default: False]
  --p-rev-comp-mapping-barcodes / --p-no-rev-comp-mapping-barcodes
                                  If provided, the barcode sequences in the
                                  sample metadata will be reverse complemented
                                  prior to demultiplexing.  [default: False]
  --o-per-sample-sequences ARTIFACT PATH SampleData[PairedEndSequencesWithQuality]
                                  The resulting demultiplexed 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.demux.methods import emp_paired

Docstring:

Demultiplex paired-end sequence data generated with the EMP protocol.

Demultiplex paired-end sequence data (i.e., map barcode reads to sample
ids) for data generated with the Earth Microbiome Project (EMP) amplicon
sequencing protocol. Details about this protocol can be found at
http://www.earthmicrobiome.org/protocols-and-standards/

Parameters
----------
seqs : EMPPairedEndSequences
    The paired-end sequences to be demultiplexed.
barcodes : MetadataColumn[Categorical]
    The sample metadata column containing the per-sample barcodes.
rev_comp_barcodes : Bool, optional
    If provided, the barcode sequence reads will be reverse complemented
    prior to demultiplexing.
rev_comp_mapping_barcodes : Bool, optional
    If provided, the barcode sequences in the sample metadata will be
    reverse complemented prior to demultiplexing.

Returns
-------
per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
    The resulting demultiplexed sequences.