Fork me on GitHub

demux-single: Demultiplex single-end sequence data with barcodes in-sequence.ΒΆ

Docstring:

Usage: qiime cutadapt demux-single [OPTIONS]

  Demultiplex sequence data (i.e., map barcode reads to sample ids).
  Barcodes are expected to be located within the sequence data (versus the
  header, or a separate barcode file).

Options:
  --i-seqs ARTIFACT PATH MultiplexedSingleEndBarcodeInSequence
                                  The single-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 listing the per-sample barcodes.
                                  [required]
  --p-error-rate FLOAT            The level of error tolerance, specified as
                                  the maximum allowable error rate. The
                                  default value specified by cutadapt is 0.1
                                  (=10%), which is greater than `demux emp-*`,
                                  which is 0.0 (=0%).  [default: 0.1]
  --o-per-sample-sequences ARTIFACT PATH SampleData[SequencesWithQuality]
                                  The resulting demultiplexed sequences.
                                  [required if not passing --output-dir]
  --o-untrimmed-sequences ARTIFACT PATH MultiplexedSingleEndBarcodeInSequence
                                  The sequences that were unmatched to
                                  barcodes.  [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.cutadapt.methods import demux_single

Docstring:

Demultiplex single-end sequence data with barcodes in-sequence.

Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
are expected to be located within the sequence data (versus the header, or
a separate barcode file).

Parameters
----------
seqs : MultiplexedSingleEndBarcodeInSequence
    The single-end sequences to be demultiplexed.
barcodes : MetadataColumn[Categorical]
    The sample metadata column listing the per-sample barcodes.
error_rate : Float % Range(0, 1, inclusive_end=True), optional
    The level of error tolerance, specified as the maximum allowable error
    rate. The default value specified by cutadapt is 0.1 (=10%), which is
    greater than `demux emp-*`, which is 0.0 (=0%).

Returns
-------
per_sample_sequences : SampleData[SequencesWithQuality]
    The resulting demultiplexed sequences.
untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
    The sequences that were unmatched to barcodes.