# NOT RUN {
## load example data
data(amplicons)
## apply filter criteria
ampliconduos.f <- filter.ampliconduo.set(amplicons)
ampliconduos.f <- filter.ampliconduo.set(amplicons, min.freq = 3, remove = TRUE)
## to return a list with the indices (corresponding to the indices of the data
## the ampliconduo function was called on) of all amplicons that passed the filter criteria
good.reads <- accepted.amplicons(ampliconduos.f)
# }
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