Fork me on GitHub

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

Docstring:

Usage: qiime cutadapt demux-paired [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).

Inputs:
  --i-seqs ARTIFACT MultiplexedPairedEndBarcodeInSequence
                          The paired-end sequences to be demultiplexed.
                                                                    [required]
Parameters:
  --m-forward-barcodes-file METADATA
  --m-forward-barcodes-column COLUMN  MetadataColumn[Categorical]
                          The sample metadata column listing the per-sample
                          barcodes for the forward reads.           [required]
  --m-reverse-barcodes-file METADATA
  --m-reverse-barcodes-column COLUMN  MetadataColumn[Categorical]
                          The sample metadata column listing the per-sample
                          barcodes for the reverse reads.           [optional]
  --p-error-rate PROPORTION Range(0, 1, inclusive_end=True)
                          The level of error tolerance, specified as the
                          maximum allowable error rate.         [default: 0.1]
  --p-batch-size INTEGER  The number of samples cutadapt demultiplexes
    Range(0, None)        concurrently. Demultiplexing in smaller batches will
                          yield the same result with marginal speed loss, and
                          may solve "too many files" errors related to sample
                          quantity. Set to "0" to process all samples at once.
                                                                  [default: 0]
Outputs:
  --o-per-sample-sequences ARTIFACT
    SampleData[PairedEndSequencesWithQuality]
                          The resulting demultiplexed sequences.    [required]
  --o-untrimmed-sequences ARTIFACT MultiplexedPairedEndBarcodeInSequence
                          The sequences that were unmatched to barcodes.
                                                                    [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).
  --citations             Show citations and exit.
  --help                  Show this message and exit.

Import:

from qiime2.plugins.cutadapt.methods import demux_paired

Docstring:

Demultiplex paired-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 : MultiplexedPairedEndBarcodeInSequence
    The paired-end sequences to be demultiplexed.
forward_barcodes : MetadataColumn[Categorical]
    The sample metadata column listing the per-sample barcodes for the
    forward reads.
reverse_barcodes : MetadataColumn[Categorical], optional
    The sample metadata column listing the per-sample barcodes for the
    reverse reads.
error_rate : Float % Range(0, 1, inclusive_end=True), optional
    The level of error tolerance, specified as the maximum allowable error
    rate.
batch_size : Int % Range(0, None), optional
    The number of samples cutadapt demultiplexes concurrently.
    Demultiplexing in smaller batches will yield the same result with
    marginal speed loss, and may solve "too many files" errors related to
    sample quantity. Set to "0" to process all samples at once.

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