A multi-item List with the following named values...
$denoised: Integer vector, named by sequence valued by abundance, of the denoised sequences.
$clustering: An informative data.frame containing information on each cluster.
$sequence: A character vector of each denoised sequence. Identical to names($denoised).
$quality: The average quality scores for each cluster (row) by position (col).
$map: Integer vector that maps the unique (index of derep$unique) to the denoised sequence (index of dada$denoised).
$birth_subs: A data.frame containing the substitutions at the birth of each new cluster.
$trans: The matrix of transitions by type (row), eg. A2A, A2C..., and quality score (col) observed in the final output of the dada algorithm.
$err_in: The err matrix used for this invocation of dada.
$err_out: The err matrix estimated from the output of dada. NULL if err_function not provided.
$opts: A list of the dada_opts used for this invocation of dada.
$call: The function call used for this invocation of dada.