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Run DADA2 denoising

Source: R/cluster.R
dada2_denoise.Rd

Runs DADA2 on a FASTQ file, removes chimeras and and returns an abundance-sorted data frame of ASVs with some additional information

Usage

dada2_denoise(
  x,
  dada_err,
  cores = 1,
  max_members = 1e+06,
  singleton_threshold = 5,
  ...
)

Arguments

x

FASTQ file path or derep-class object

dada_err

error information returned by dada_learn_errors

max_members

do random subsampling of overly large ASVs to the specified number of sequences

singleton_threshold

by default, singletons cannot form a new cluster, but for very low-depth samples (< N duplicates of any sequence), DETECT_SINGLETONS is turned on (see dada2::setDadaOpt). This increases sensitivity with InDel-rich Nanopore data and prevents that a large proportion of sequences are discarded.

...

Arguments passed to dada2::dada

Value

a data frame with the following columns:

  • sequence

  • top_uniques: abundance of top unique sequences