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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.

Inputs:
  --i-demux ARTIFACT SampleData[JoinedSequencesWithQuality]
                       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[JoinedSequencesWithQuality]
                       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).
  --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.