q-score: Quality filter based on sequence quality scores.¶

Docstring:

Usage: qiime quality-filter q-score [OPTIONS]

  This method filters sequence based on quality scores and the presence of
  ambiguous base calls.

Inputs:
  --i-demux ARTIFACT SampleData[SequencesWithQuality |
    PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²
                         The demultiplexed sequence data to be quality
                         filtered.                                  [required]
Parameters:
  --p-min-quality INTEGER
                         The minimum acceptable PHRED score. All PHRED scores
                         less that this value are considered to be low PHRED
                         scores.                                  [default: 4]
  --p-quality-window INTEGER
                         The maximum number of low PHRED scores that can be
                         observed in direct succession before truncating a
                         sequence read.                           [default: 3]
  --p-min-length-fraction NUMBER
                         The minimum length that a sequence read can be
                         following truncation and still be retained. This
                         length should be provided as a fraction of the input
                         sequence length.                      [default: 0.75]
  --p-max-ambiguous INTEGER
                         The maximum number of ambiguous (i.e., N) base
                         calls. This is applied after trimming sequences based
                         on `min-length-fraction`.                [default: 0]
Outputs:
  --o-filtered-sequences ARTIFACT SampleData[SequencesWithQuality]¹ |
    SampleData[JoinedSequencesWithQuality]²
                         The resulting quality-filtered sequences.  [required]
  --o-filter-stats ARTIFACT
    QualityFilterStats   Summary statistics of the filtering process.
                                                                    [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: q score
  qiime quality-filter q-score \
    --i-demux demuxed-seqs.qza \
    --o-filtered-sequences dumux-filtered.qza \
    --o-filter-stats demux-filter-stats.qza