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denoise-paired: Denoise and dereplicate paired-end sequencesΒΆ

Docstring:

Usage: qiime dada2 denoise-paired [OPTIONS]

  This method denoises paired-end sequences, dereplicates them, and filters
  chimeras.

Options:
  --i-demultiplexed-seqs ARTIFACT PATH SampleData[PairedEndSequencesWithQuality]
                                  The paired-end demultiplexed sequences to be
                                  denoised.  [required]
  --p-trunc-len-f INTEGER         Position at which forward read sequences
                                  should be truncated due to decrease in
                                  quality. This truncates the 3' end of the of
                                  the input sequences, which will be the bases
                                  that were sequenced in the last cycles.
                                  Reads that are shorter than this value will
                                  be discarded. After this parameter is
                                  applied there must still be at least a 20
                                  nucleotide overlap between the forward and
                                  reverse reads. If 0 is provided, no
                                  truncation or length filtering will be
                                  performed  [required]
  --p-trunc-len-r INTEGER         Position at which reverse read sequences
                                  should be truncated due to decrease in
                                  quality. This truncates the 3' end of the of
                                  the input sequences, which will be the bases
                                  that were sequenced in the last cycles.
                                  Reads that are shorter than this value will
                                  be discarded. After this parameter is
                                  applied there must still be at least a 20
                                  nucleotide overlap between the forward and
                                  reverse reads. If 0 is provided, no
                                  truncation or length filtering will be
                                  performed  [required]
  --p-trim-left-f INTEGER         Position at which forward read sequences
                                  should be trimmed due to low quality. This
                                  trims the 5' end of the input sequences,
                                  which will be the bases that were sequenced
                                  in the first cycles.  [default: 0]
  --p-trim-left-r INTEGER         Position at which reverse read sequences
                                  should be trimmed due to low quality. This
                                  trims the 5' end of the input sequences,
                                  which will be the bases that were sequenced
                                  in the first cycles.  [default: 0]
  --p-max-ee FLOAT                Reads with number of expected errors higher
                                  than this value will be discarded.
                                  [default: 2.0]
  --p-trunc-q INTEGER             Reads are truncated at the first instance of
                                  a quality score less than or equal to this
                                  value. If the resulting read is then shorter
                                  than `trunc_len_f` or `trunc_len_r`
                                  (depending on the direction of the read) it
                                  is discarded.  [default: 2]
  --p-chimera-method [consensus|pooled|none]
                                  The method used to remove chimeras. "none":
                                  No chimera removal is performed. "pooled":
                                  All reads are pooled prior to chimera
                                  detection. "consensus": Chimeras are
                                  detected in samples individually, and
                                  sequences found chimeric in a sufficient
                                  fraction of samples are removed.  [default:
                                  consensus]
  --p-min-fold-parent-over-abundance FLOAT
                                  The minimum abundance of potential parents
                                  of a sequence being tested as chimeric,
                                  expressed as a fold-change versus the
                                  abundance of the sequence being tested.
                                  Values should be greater than or equal to 1
                                  (i.e. parents should be more abundant than
                                  the sequence being tested). This parameter
                                  has no effect if chimera_method is "none".
                                  [default: 1.0]
  --p-n-threads INTEGER           The number of threads to use for
                                  multithreaded processing. If 0 is provided,
                                  all available cores will be used.  [default:
                                  1]
  --p-n-reads-learn INTEGER       The number of reads to use when training the
                                  error model. Smaller numbers will result in
                                  a shorter run time but a less reliable error
                                  model.  [default: 1000000]
  --p-hashed-feature-ids / --p-no-hashed-feature-ids
                                  If true, the feature ids in the resulting
                                  table will be presented as hashes of the
                                  sequences defining each feature. The hash
                                  will always be the same for the same
                                  sequence so this allows feature tables to be
                                  merged across runs of this method. You
                                  should only merge tables if the exact same
                                  parameters are used for each run.  [default:
                                  True]
  --o-table ARTIFACT PATH FeatureTable[Frequency]
                                  The resulting feature table.  [required if
                                  not passing --output-dir]
  --o-representative-sequences ARTIFACT PATH FeatureData[Sequence]
                                  The resulting feature sequences. Each
                                  feature in the feature table will be
                                  represented by exactly one sequence, and
                                  these sequences will be the joined paired-
                                  end sequences.  [required if not passing
                                  --output-dir]
  --o-denoising-stats ARTIFACT PATH SampleData[DADA2Stats]
                                  [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.dada2.methods import denoise_paired

Docstring:

Denoise and dereplicate paired-end sequences

This method denoises paired-end sequences, dereplicates them, and filters
chimeras.

Parameters
----------
demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
    The paired-end demultiplexed sequences to be denoised.
trunc_len_f : Int
    Position at which forward read sequences should be truncated due to
    decrease in quality. This truncates the 3' end of the of the input
    sequences, which will be the bases that were sequenced in the last
    cycles. Reads that are shorter than this value will be discarded. After
    this parameter is applied there must still be at least a 20 nucleotide
    overlap between the forward and reverse reads. If 0 is provided, no
    truncation or length filtering will be performed
trunc_len_r : Int
    Position at which reverse read sequences should be truncated due to
    decrease in quality. This truncates the 3' end of the of the input
    sequences, which will be the bases that were sequenced in the last
    cycles. Reads that are shorter than this value will be discarded. After
    this parameter is applied there must still be at least a 20 nucleotide
    overlap between the forward and reverse reads. If 0 is provided, no
    truncation or length filtering will be performed
trim_left_f : Int, optional
    Position at which forward read sequences should be trimmed due to low
    quality. This trims the 5' end of the input sequences, which will be
    the bases that were sequenced in the first cycles.
trim_left_r : Int, optional
    Position at which reverse read sequences should be trimmed due to low
    quality. This trims the 5' end of the input sequences, which will be
    the bases that were sequenced in the first cycles.
max_ee : Float, optional
    Reads with number of expected errors higher than this value will be
    discarded.
trunc_q : Int, optional
    Reads are truncated at the first instance of a quality score less than
    or equal to this value. If the resulting read is then shorter than
    `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
    it is discarded.
chimera_method : Str % Choices({'consensus', 'none', 'pooled'}), optional
    The method used to remove chimeras. "none": No chimera removal is
    performed. "pooled": All reads are pooled prior to chimera detection.
    "consensus": Chimeras are detected in samples individually, and
    sequences found chimeric in a sufficient fraction of samples are
    removed.
min_fold_parent_over_abundance : Float, optional
    The minimum abundance of potential parents of a sequence being tested
    as chimeric, expressed as a fold-change versus the abundance of the
    sequence being tested. Values should be greater than or equal to 1
    (i.e. parents should be more abundant than the sequence being tested).
    This parameter has no effect if chimera_method is "none".
n_threads : Int, optional
    The number of threads to use for multithreaded processing. If 0 is
    provided, all available cores will be used.
n_reads_learn : Int, optional
    The number of reads to use when training the error model. Smaller
    numbers will result in a shorter run time but a less reliable error
    model.
hashed_feature_ids : Bool, optional
    If true, the feature ids in the resulting table will be presented as
    hashes of the sequences defining each feature. The hash will always be
    the same for the same sequence so this allows feature tables to be
    merged across runs of this method. You should only merge tables if the
    exact same parameters are used for each run.

Returns
-------
table : FeatureTable[Frequency]
    The resulting feature table.
representative_sequences : FeatureData[Sequence]
    The resulting feature sequences. Each feature in the feature table will
    be represented by exactly one sequence, and these sequences will be the
    joined paired-end sequences.
denoising_stats : SampleData[DADA2Stats]