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filter-reads: Filter demultiplexed sequences by alignment to reference database.

Citations

Docstring:

Usage: qiime quality-control filter-reads [OPTIONS]

  Filter out (or keep) demultiplexed single- or paired-end sequences that
  align to a reference database, using bowtie2 and samtools. This method can
  be used to filter out human DNA sequences and other contaminants in any
  FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
  alternatively (when exclude_seqs is False) to only keep sequences that do
  align to the reference.

Inputs:
  --i-demultiplexed-sequences ARTIFACT SampleData[SequencesWithQuality¹ |
    PairedEndSequencesWithQuality²]
                         The sequences to be trimmed.               [required]
  --i-database ARTIFACT  Bowtie2 indexed database.
    Bowtie2Index                                                    [required]
Parameters:
  --p-n-threads INTEGER  Number of alignment threads to launch.
    Range(1, None)                                                [default: 1]
  --p-mode TEXT Choices('local', 'global')
                         Bowtie2 alignment settings. See bowtie2 manual for
                         more details.                      [default: 'local']
  --p-sensitivity TEXT Choices('very-fast', 'fast', 'sensitive',
    'very-sensitive')    Bowtie2 alignment sensitivity. See bowtie2 manual
                         for details.                   [default: 'sensitive']
  --p-ref-gap-open-penalty INTEGER
    Range(1, None)       Reference gap open penalty.              [default: 5]
  --p-ref-gap-ext-penalty INTEGER
    Range(1, None)       Reference gap extend penalty.            [default: 3]
  --p-exclude-seqs / --p-no-exclude-seqs
                         Exclude sequences that align to reference. Set this
                         option to False to exclude sequences that do not
                         align to the reference database.      [default: True]
Outputs:
  --o-filtered-sequences ARTIFACT SampleData[SequencesWithQuality¹ |
    PairedEndSequencesWithQuality²]
                         The resulting filtered sequences.          [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).
  --examples             Show usage examples and exit.
  --citations            Show citations and exit.
  --help                 Show this message and exit.

Import:

from qiime2.plugins.quality_control.methods import filter_reads

Docstring:

Filter demultiplexed sequences by alignment to reference database.

Filter out (or keep) demultiplexed single- or paired-end sequences that
align to a reference database, using bowtie2 and samtools. This method can
be used to filter out human DNA sequences and other contaminants in any
FASTQ sequence data (e.g., shotgun genome or amplicon sequence data), or
alternatively (when exclude_seqs is False) to only keep sequences that do
align to the reference.

Parameters
----------
demultiplexed_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
    The sequences to be trimmed.
database : Bowtie2Index
    Bowtie2 indexed database.
n_threads : Int % Range(1, None), optional
    Number of alignment threads to launch.
mode : Str % Choices('local', 'global'), optional
    Bowtie2 alignment settings. See bowtie2 manual for more details.
sensitivity : Str % Choices('very-fast', 'fast', 'sensitive', 'very-sensitive'), optional
    Bowtie2 alignment sensitivity. See bowtie2 manual for details.
ref_gap_open_penalty : Int % Range(1, None), optional
    Reference gap open penalty.
ref_gap_ext_penalty : Int % Range(1, None), optional
    Reference gap extend penalty.
exclude_seqs : Bool, optional
    Exclude sequences that align to reference. Set this option to False to
    exclude sequences that do not align to the reference database.

Returns
-------
filtered_sequences : SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality²]
    The resulting filtered sequences.