This performs the following steps:
Learning the error rate for each run separately
Inferring sequence variants for each run and sample
Merging of feature tables across runs
Consensus chimera removal
Taxa assignment with Naive Bayes
Species assignment by exact alignment
Diagnostic plots of the error rates
You will usually want to preprocess the read files first with
preprocess
.
Depending on your config the sequences might be represented by
an MD5 hash. In this case the taxa table has an additional `sequence` column
containing the real sequences.
denoise(object, ...)
object | An experiment data table as returned by
|
---|---|
... | A configuration as returned by
|
A list containing the workflow results:
Matrix of sequence variant abundances. Samples are and sequences are columns.
Matrix of taxonomy assignments. Rows are sequences and columns are taxonomy ranks.
The error profiles estimated by DADA2. One for each run and read direction (forward/reverse).
Plotted error profiles. One for each run and read direction (forward/reverse).
How many reads were kept in each step. Rows are samples and columns are workflow steps.
The proportion of sequence variants that could be where a specific taxa rank could be classified.