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-forward-cut INTEGER Remove the specified number of bases from the
forward 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. If
--p-mixed-orientation is set, then both
--p-forward-cut and --p-reverse-cut must be set to
the same value. [default: 0]
--p-reverse-cut INTEGER Remove the specified number of bases from the
reverse 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. If
--p-mixed-orientation is set, then both
--p-forward-cut and --p-reverse-cut must be set to
the same value. [default: 0]
--p-anchor-forward-barcode / --p-no-anchor-forward-barcode
Anchor the forward barcode. The barcode is then
expected to occur in full length at the beginning
(5' end) of the forward sequence. Can speed up
demultiplexing if used. [default: False]
--p-anchor-reverse-barcode / --p-no-anchor-reverse-barcode
Anchor the reverse barcode. The barcode is then
expected to occur in full length at the beginning
(5' end) of the reverse 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. [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-mixed-orientation / --p-no-mixed-orientation
Handle demultiplexing of mixed orientation reads
(i.e. when forward and reverse reads coexist in the
same file). [default: False]
--p-cores NTHREADS Number of CPU cores to use. [default: 1]
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).
--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: paired
qiime cutadapt demux-paired \
--i-seqs seqs.qza \
--m-forward-barcodes-file md.tsv \
--m-forward-barcodes-column barcode-sequence \
--o-per-sample-sequences per-sample-sequences.qza \
--o-untrimmed-sequences untrimmed-sequences.qza
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.
forward_cut : Int, optional
Remove the specified number of bases from the forward 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. If
--p-mixed-orientation is set, then both --p-forward-cut and
--p-reverse-cut must be set to the same value.
reverse_cut : Int, optional
Remove the specified number of bases from the reverse 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. If
--p-mixed-orientation is set, then both --p-forward-cut and
--p-reverse-cut must be set to the same value.
anchor_forward_barcode : Bool, optional
Anchor the forward barcode. The barcode is then expected to occur in
full length at the beginning (5' end) of the forward sequence. Can
speed up demultiplexing if used.
anchor_reverse_barcode : Bool, optional
Anchor the reverse barcode. The barcode is then expected to occur in
full length at the beginning (5' end) of the reverse 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.
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.
mixed_orientation : Bool, optional
Handle demultiplexing of mixed orientation reads (i.e. when forward and
reverse reads coexist in the same file).
cores : Threads, optional
Number of CPU cores to use.
Returns
-------
per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
The resulting demultiplexed sequences.
untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
The sequences that were unmatched to barcodes.
