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).
Inputs:
--i-seqs ARTIFACT MultiplexedSingleEndBarcodeInSequence
The single-end sequences to be demultiplexed.
[required]
Parameters:
--m-barcodes-file METADATA
--m-barcodes-column COLUMN MetadataColumn[Categorical]
The sample metadata column listing the per-sample
barcodes. [required]
--p-cut INTEGER Remove the specified number of bases from the
sequences. Bases are removed before demultiplexing.
If a positive value is provided, bases are removed
from the beginning of the sequences. If a negative
value is provided, bases are removed from the end of
the sequences. [default: 0]
--p-anchor-barcode / --p-no-anchor-barcode
Anchor the barcode. The barcode is then expected to
occur in full length at the beginning (5' end) of
the sequence. Can speed up demultiplexing if used.
[default: False]
--p-error-rate PROPORTION Range(0, 1, inclusive_end=True)
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]
--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]
--p-minimum-length INTEGER
Range(1, None) Discard reads shorter than specified value. Note,
the cutadapt default of 0 has been overridden,
because that value produces empty sequence records.
[default: 1]
--p-cores NTHREADS Number of CPU cores to use. [default: 1]
Outputs:
--o-per-sample-sequences ARTIFACT SampleData[SequencesWithQuality]
The resulting demultiplexed sequences. [required]
--o-untrimmed-sequences ARTIFACT MultiplexedSingleEndBarcodeInSequence
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).
--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 single
qiime cutadapt demux-single \
--i-seqs seqs.qza \
--m-barcodes-file md.tsv \
--m-barcodes-column BarcodeSequence \
--o-per-sample-sequences per-sample-sequences.qza \
--o-untrimmed-sequences untrimmed-sequences.qza
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.
cut : Int, optional
Remove the specified number of bases from the sequences. Bases are
removed before demultiplexing. If a positive value is provided, bases
are removed from the beginning of the sequences. If a negative value is
provided, bases are removed from the end of the sequences.
anchor_barcode : Bool, optional
Anchor the barcode. The barcode is then expected to occur in full
length at the beginning (5' end) of the sequence. Can speed up
demultiplexing if used.
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%).
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.
minimum_length : Int % Range(1, None), optional
Discard reads shorter than specified value. Note, the cutadapt default
of 0 has been overridden, because that value produces empty sequence
records.
cores : Threads, optional
Number of CPU cores to use.
Returns
-------
per_sample_sequences : SampleData[SequencesWithQuality]
The resulting demultiplexed sequences.
untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
The sequences that were unmatched to barcodes.
