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

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