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emp-single: Demultiplex sequence data generated with the EMP protocol.¶
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Docstring:
Usage: qiime demux emp-single [OPTIONS]
Demultiplex 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 RawSequences | EMPSingleEndSequences |
EMPPairedEndSequences
The single-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[SequencesWithQuality]
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.
Examples:
# ### example: demux
qiime demux emp-single \
--i-seqs sequences.qza \
--m-barcodes-file sample-metadata.tsv \
--m-barcodes-column barcode-sequence \
--o-per-sample-sequences demux.qza \
--o-error-correction-details demux-details.qza
Import:
from qiime2.plugins.demux.methods import emp_single
Docstring:
Demultiplex sequence data generated with the EMP protocol.
Demultiplex 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 : RawSequences | EMPSingleEndSequences | EMPPairedEndSequences
The single-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[SequencesWithQuality]
The resulting demultiplexed sequences.
error_correction_details : ErrorCorrectionDetails
Detail about the barcode error corrections.