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

Citations
  • Micah Hamday and Rob Knight. Microbial community profiling for human microbiome projects: tools, techniques, and challenges. Genome Research, 19:1141–1152, 2009. doi:10.1101/gr.085464.108.

  • Micah Hamday, Jeffrey Walker J., J. Kirk Harris, Nicholas Gold J., and Rob Knight. Error-correcting barcoded primers allow hundreds of samples to be pyrosequenced in multiplex. Nature Methods, 5:235––237, 2008. doi:10.1038/nmeth.1184.

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/

Inputs:
  --i-seqs ARTIFACT EMPPairedEndSequences
                       The paired-end sequences to be demultiplexed.
                                                                    [required]
Parameters:
  --m-barcodes-file METADATA
  --m-barcodes-column COLUMN  MetadataColumn[Categorical]
                       The sample metadata column containing the per-sample
                       barcodes.                                    [required]
  --p-golay-error-correction / --p-no-golay-error-correction
                       Perform 12nt Golay error correction on the barcode
                       reads.                                  [default: True]
  --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]
Outputs:
  --o-per-sample-sequences ARTIFACT
    SampleData[PairedEndSequencesWithQuality]
                       The resulting demultiplexed sequences.       [required]
  --o-error-correction-details ARTIFACT ErrorCorrectionDetails
                       Detail about the barcode error corrections.  [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.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.
golay_error_correction : Bool, optional
    Perform 12nt Golay error correction on the barcode reads.
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.
error_correction_details : ErrorCorrectionDetails
    Detail about the barcode error corrections.