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

Docstring:

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

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

Options:
  --i-demux ARTIFACT PATH SampleData[JoinedSequencesWithQuality]
                                  The demultiplexed sequence data to be
                                  quality filtered.  [required]
  --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 FLOAT   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]
  --o-filtered-sequences ARTIFACT PATH SampleData[JoinedSequencesWithQuality]
                                  The resulting quality-filtered sequences.
                                  [required if not passing --output-dir]
  --o-filter-stats ARTIFACT PATH QualityFilterStats
                                  Summary statistics of the filtering process.
                                  [required if not passing --output-dir]
  --output-dir DIRECTORY          Output unspecified results to a directory
  --cmd-config FILE               Use config file for command options
  --verbose                       Display verbose output to stdout and/or
                                  stderr during execution of this action.
                                  [default: False]
  --quiet                         Silence output if execution is successful
                                  (silence is golden).  [default: False]
  --citations                     Show citations and exit.
  --help                          Show this message and exit.

Import:

from qiime2.plugins.quality_filter.methods import q_score_joined

Docstring:

Quality filter based on joined sequence quality scores.

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

Parameters
----------
demux : SampleData[JoinedSequencesWithQuality]
    The demultiplexed sequence data to be quality filtered.
min_quality : Int, optional
    The minimum acceptable PHRED score. All PHRED scores less that this
    value are considered to be low PHRED scores.
quality_window : Int, optional
    The maximum number of low PHRED scores that can be observed in direct
    succession before truncating a sequence read.
min_length_fraction : Float, optional
    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.
max_ambiguous : Int, optional
    The maximum number of ambiguous (i.e., N) base calls. This is applied
    after trimming sequences based on `min_length_fraction`.

Returns
-------
filtered_sequences : SampleData[JoinedSequencesWithQuality]
    The resulting quality-filtered sequences.
filter_stats : QualityFilterStats
    Summary statistics of the filtering process.