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
Import:
from qiime2.plugins.quality_filter.methods import q_score
Docstring:
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]¹ | SampleData[JoinedSequencesWithQuality]²
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]¹ | SampleData[JoinedSequencesWithQuality]²
The resulting quality-filtered sequences.
filter_stats : QualityFilterStats
Summary statistics of the filtering process.
