derepMulti: derepMulti

In derele/MultiAmplicon: Metabarcoding and microbiome analysis using multiple amplicons

derepMulti

Description

Dereplicate sequences in fastq files.

Usage

derepMulti(
  MA,
  mc.cores = getOption("mc.cores", 1L),
  keep.single.singlets = FALSE,
  ...
)

Arguments

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 TRUE) might result in downstream problems (Errors) in dada inference.
...	arguments to be passed to derepFastq. All arguments to the function can be given as a vector of the same length as the number of primer pairs in the MultiAmplicon object, allowing to specify different parameters for each amplicon. If a shorter vector is given it will be recycled to match the number of amplicons. A general argument to consider changing is n (default 1e+06, the maximum number of reads to parse at one time). Smaller values will decreas memory consumption.

Details

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).

Value

MultiAmplicon object with paired derep slot (forward derepF and reverse derepR) filled.

Author(s)

Emanuel Heitlinger

derele/MultiAmplicon documentation built on Oct. 14, 2023, 7:43 p.m.