qiime quality-filter q-score (version 2019.4)

--i-demux: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality] 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: 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]:

Quality filter based on sequence quality scores.

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

Parameters

demux : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]: 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[SequencesWithQuality]: The resulting quality-filtered sequences.
filter_stats : QualityFilterStats: Summary statistics of the filtering process.