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denoise-16S: Deblur sequences using a 16S positive filter.ΒΆ

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 INTEGER
                         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).
  --citations            Show citations and exit.
  --help                 Show this message and exit.

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 : Int, 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.