setDadaOpt sets the default options used by the dada(...) function for your current session, much
par sets the session default plotting parameters. However, all dada options can be set as
part of the dada(...) function call itself by including a DADA_OPTION_NAME=VALUE argument.
(Required). The DADA options to set, along with their new value.
The various dada options...
OMEGA_A: This parameter sets the threshold for when DADA2 calls unique sequences significantly overabundant, and therefore creates a new cluster with that sequence as the center. The default value is 1e-40, which is a conservative setting to avoid making false positive inferences, but which comes at the cost of reducing the ability to identify some rare variants.
USE_QUALS: If TRUE, the dada(...) error model takes into account the consensus quality score of the dereplicated unique sequences. If FALSE, quality scores are ignored. The default is TRUE, however if applying DADA2 to pyrosequenced data it is recommended to set USE_QUALS to FALSE, as quality scores are not informative about substitution error rates in pyrosequencing.
USE_KMERS: If TRUE, a 5-mer distance screen is performed prior to performing each pairwise alignment, and if the 5mer-distance is greater than KDIST_CUTOFF, no alignment is performed. TRUE by default.
KDIST_CUTOFF: The default value of 0.42 was chosen to screen pairs of sequences that differ by >10%, and was calibrated on Illumina sequenced 16S amplicon data. The assumption is that sequences that differ by such a large amount cannot be linked by amplicon errors (i.e. if you sequence one, you won't get a read of other) and so careful (and costly) alignment is unnecessary.
BAND_SIZE: When set, banded Needleman-Wunsch alignments are performed. Banding restricts the net cumulative number of insertion of one sequence relative to the other. The default value of BAND_SIZE is 16. If DADA is applied to marker genes with high rates of indels, such as the ITS region in fungi, the BAND_SIZE parameter should be increased. Setting BAND_SIZE to a negative number turns off banding (i.e. full Needleman-Wunsch).
SCORE_MATRIX: The score matrix for the Needleman-Wunsch alignment. This is a 4x4 matrix as no ambiguous nucleotides are allowed. Default is nuc44: -4 for mismatches, +5 for matches.
GAP_PENALTY: The cost of gaps in the Needleman-Wunsch alignment. Default is -8.
HOMOPOLYMER_GAP_PENALTY: The cost of gaps in homopolymer regions (>=3 repeated bases). Default is NULL, which causes homopolymer gaps to be treated as normal gaps.
MIN_FOLD: The minimum fold-overabundance for sequences to form new clusters. Default value is 1, which means this criteria is ignored.
MIN_HAMMING: The minimum hamming-separation for sequences to form new clusters. Default value is 1, which means this criteria is ignored.
MAX_CLUST: The maximum number of clusters. Once this many clusters have been created, the algorithm terminates regardless of whether the statistical model suggests more sample sequences exist. If set to 0 this argument is ignored. Default value is 0.
MAX_CONSIST: The maximum number of steps when selfConsist=TRUE. If convergence is not reached in MAX_CONSIST steps, the algorithm will terminate with a warning message. Default value is 10.
VERBOSE: If TRUE progress messages from the algorithm are printed. Warning: There is a lot of output. Default is FALSE.
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