PrimerStrip: PrimerStrip

In leholman/metabarTOAD: A group of simple functions for handling metabarcoding data

PrimerStrip

Description

This function uses cutadapt to strip off non-biological nucleotides (adapters or primers) from fastq files. It depends on Cutadapt.

Usage

PrimerStrip(
  PrimerF = NA,
  PrimerR = NA,
  MinLen = NA,
  MaxLen = NA,
  UsePrimerFile = FALSE,
  folderwfiles = "2.mergedreads",
  folderoutput = "3.strippedreads",
  cutadaptdest = "cutadapt",
  ncores = 1
)

Arguments

PrimerF	The 5-3 sequence of the forward primer. Ambiguous sequences are accepted (eg.N).
PrimerR	The 5-3 sequence of the reverse primer. Ambiguous sequences are accepted (eg.N).
MinLen	Minimum sequence length to be retained.
MaxLen	Maximum sequence length to be retained.
UsePrimerFile	TRUE or FALSE, is a csv file provided containing primer information?
folderwfiles	A directory indicating files to be processed if not default folder.
folderoutput	Output directory.
cutadaptdest	Full directory for the cutadapt executable if not in PATH.
ncores	Number of processsor cores to use.

Value

None

leholman/metabarTOAD documentation built on Aug. 27, 2023, 9:07 p.m.