Docstring:
Usage: qiime deblur denoise-16S [OPTIONS]
Perform sequence quality control for Illumina data using the Deblur workflow
with a 16S reference as a positive filter. Only forward reads are supported
at this time. The specific reference used is the 88% OTUs from Greengenes
13_8. This mode of operation should only be used when data were generated
from a 16S amplicon protocol on an Illumina platform. The reference is only
used to assess whether each sequence is likely to be 16S by a local
alignment using SortMeRNA with a permissive e-value; the reference is not
used to characterize the sequences.
Inputs:
--i-demultiplexed-seqs ARTIFACT SampleData[SequencesWithQuality |
PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
The demultiplexed sequences to be denoised.
[required]
Parameters:
--p-trim-length INTEGER
Sequence trim length, specify -1 to disable
trimming. [required]
--p-left-trim-len INTEGER
Range(0, None) Sequence trimming from the 5' end. A value of 0 will
disable this trim. [default: 0]
--p-sample-stats / --p-no-sample-stats
If true, gather stats per sample. [default: False]
--p-mean-error NUMBER The mean per nucleotide error, used for original
sequence estimate. [default: 0.005]
--p-indel-prob NUMBER Insertion/deletion (indel) probability (same for N
indels). [default: 0.01]
--p-indel-max INTEGER Maximum number of insertion/deletions. [default: 3]
--p-min-reads INTEGER Retain only features appearing at least min-reads
times across all samples in the resulting feature
table. [default: 10]
--p-min-size INTEGER In each sample, discard all features with an
abundance less than min-size. [default: 2]
--p-jobs-to-start NTHREADS
Number of jobs to start (if to run in parallel).
[default: 1]
--p-hashed-feature-ids / --p-no-hashed-feature-ids
If true, hash the feature IDs. [default: True]
Outputs:
--o-table ARTIFACT FeatureTable[Frequency]
The resulting denoised feature table. [required]
--o-representative-sequences ARTIFACT FeatureData[Sequence]
The resulting feature sequences. [required]
--o-stats ARTIFACT Per-sample stats if requested.
DeblurStats [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: denoise 16S
qiime deblur denoise-16S \
--i-demultiplexed-seqs demux-filtered.qza \
--p-trim-length 120 \
--p-sample-stats \
--o-representative-sequences representative-sequences.qza \
--o-table table.qza \
--o-stats denoising-stats.qza
Import:
from qiime2.plugins.deblur.methods import denoise_16S
Docstring:
Deblur sequences using a 16S positive filter.
Perform sequence quality control for Illumina data using the Deblur
workflow with a 16S reference as a positive filter. Only forward reads are
supported at this time. The specific reference used is the 88% OTUs from
Greengenes 13_8. This mode of operation should only be used when data were
generated from a 16S amplicon protocol on an Illumina platform. The
reference is only used to assess whether each sequence is likely to be 16S
by a local alignment using SortMeRNA with a permissive e-value; the
reference is not used to characterize the sequences.
Parameters
----------
demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
The demultiplexed sequences to be denoised.
trim_length : Int
Sequence trim length, specify -1 to disable trimming.
left_trim_len : Int % Range(0, None), optional
Sequence trimming from the 5' end. A value of 0 will disable this trim.
sample_stats : Bool, optional
If true, gather stats per sample.
mean_error : Float, optional
The mean per nucleotide error, used for original sequence estimate.
indel_prob : Float, optional
Insertion/deletion (indel) probability (same for N indels).
indel_max : Int, optional
Maximum number of insertion/deletions.
min_reads : Int, optional
Retain only features appearing at least min_reads times across all
samples in the resulting feature table.
min_size : Int, optional
In each sample, discard all features with an abundance less than
min_size.
jobs_to_start : Threads, optional
Number of jobs to start (if to run in parallel).
hashed_feature_ids : Bool, optional
If true, hash the feature IDs.
Returns
-------
table : FeatureTable[Frequency]
The resulting denoised feature table.
representative_sequences : FeatureData[Sequence]
The resulting feature sequences.
stats : DeblurStats
Per-sample stats if requested.
