Dereplicate sequences in fastq files.
derepMulti( MA, mc.cores = getOption("mc.cores", 1L), keep.single.singlets = FALSE, ... )
MA | MultiAmplicon object to be dereplicated. |
---|---|
mc.cores | number or compute cores for parallel dereplication of different amplicons (values > 1 are only allowed on Unix/Linux systems). |
keep.single.singlets | logical argument indicating whether a
derep slot should be filled with a single sequence recovered
in only one sample. Defaults to FALSE meaning that empty derep
objects are created in such a case. Keeping instead single
sequence derep objects (setting this to |
... | arguments to be passed to
|
MultiAmplicon object with paired derep slot (forward derepF and reverse derepR) filled.
An interface to derepFastq
, which itself uses
FastqStreamer
for dereplicating amplicon
sequences from fastq or compressed fastq
files. FastqStreamer
uses a streaming
interface and can be used on low memory machines (see ...
below).
Emanuel Heitlinger