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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]
  --p-ignore-description-mismatch / --p-no-ignore-description-mismatch
                         If enabled, ignore mismatches in sequence record
                         description fields.                  [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).
  --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.

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.
ignore_description_mismatch : Bool, optional
    If enabled, ignore mismatches in sequence record description fields.

Returns
-------
per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
    The resulting demultiplexed sequences.
error_correction_details : ErrorCorrectionDetails
    Detail about the barcode error corrections.