Qiime2 DADA2使用参数

qiime dada2 denoise-paired --help

Usage: qiime dada2 denoise-paired [OPTIONS]

  This method denoises paired-end sequences, dereplicates them, and filters
  chimeras.
  该方法对双末端测序数据进行去噪、去重复、以及过滤嵌合体。

Inputs:
  --i-demultiplexed-seqs ARTIFACT SampleData[PairedEndSequencesWithQuality]
                         The paired-end demultiplexed sequences to be
                         denoised.                                  [required]
Parameters:
  --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 12 nucleotide overlap between the
                         forward and reverse reads. If 0 is provided, no
                         truncation or length filtering will be performed
                                                                    [required]
由于质量下降，正向read序列应该被截断的位置。这将截断输入序列的3'端，这将是在最后一个循环中被测序的碱基。低于该值的reads将被丢弃。使用该参数后，在正向和反向reads之间必须至少有12个核苷酸重叠。如果设置为0，则不进行截断或长度过滤。
  --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 12 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]
由于低质量，正向read序列应该被裁剪的位置。这将裁剪输入序列的5'端，这将是在第一个循环中测序的的碱基。
  --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-f NUMBER    Forward reads with number of expected errors higher
                         than this value will be discarded.     [default: 2.0]
  --p-max-ee-r NUMBER    Reverse 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-pooling-method TEXT Choices('independent', 'pseudo')
                         The method used to pool samples for denoising.
                         "independent": Samples are denoised indpendently.
                         "pseudo": The pseudo-pooling method is used to
                         approximate pooling of samples. In short, samples are
                         denoised independently once, ASVs detected in at
                         least 2 samples are recorded, and samples are
                         denoised independently a second time, but this time
                         with prior knowledge of the recorded ASVs and thus
                         higher sensitivity to those ASVs.
                                                      [default: 'independent']
  --p-chimera-method TEXT Choices('consensus', 'none', 'pooled')
                         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 NUMBER
                         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]
Outputs:
  --o-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table.               [required]
  --o-representative-sequences ARTIFACT 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]
  --o-denoising-stats ARTIFACT SampleData[DADA2Stats]
                                                                    [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.

qiime dada2 denoise-single --help

Usage: qiime dada2 denoise-single [OPTIONS]

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

Inputs:
  --i-demultiplexed-seqs ARTIFACT SampleData[SequencesWithQuality |
    PairedEndSequencesWithQuality]
                         The single-end demultiplexed sequences to be
                         denoised.                                  [required]
Parameters:
  --p-trunc-len INTEGER  Position at which 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. If 0
                         is provided, no truncation or length filtering will
                         be performed                               [required]
  --p-trim-left INTEGER  Position at which sequences should be trimmed due to
                         low quality. This trims the 5' end of the of the
                         input sequences, which will be the bases that were
                         sequenced in the first cycles.           [default: 0]
  --p-max-ee NUMBER      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`,
                         it is discarded.                         [default: 2]
  --p-pooling-method TEXT Choices('independent', 'pseudo')
                         The method used to pool samples for denoising.
                         "independent": Samples are denoised independently.
                         "pseudo": The pseudo-pooling method is used to
                         approximate pooling of samples. In short, samples are
                         denoised independently once, ASVs detected in at
                         least 2 samples are recorded, and samples are
                         denoised independently a second time, but this time
                         with prior knowledge of the recorded ASVs and thus
                         higher sensitivity to those ASVs.
                                                      [default: 'independent']
  --p-chimera-method TEXT Choices('consensus', 'none', 'pooled')
                         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 NUMBER
                         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]
Outputs:
  --o-table ARTIFACT FeatureTable[Frequency]
                         The resulting feature table.               [required]
  --o-representative-sequences ARTIFACT FeatureData[Sequence]
                         The resulting feature sequences. Each feature in the
                         feature table will be represented by exactly one
                         sequence.                                  [required]
  --o-denoising-stats ARTIFACT SampleData[DADA2Stats]
                                                                    [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.