cut_trim: Main command to trim primers using 'Cutadapt' and core...

In demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

Main command to trim primers using 'Cutadapt' and core 'DADA2' functions

Description

Main command to trim primers using 'Cutadapt' and core 'DADA2' functions

Usage

cut_trim(analysis_setup, cutadapt_path, overwrite_existing = FALSE)

Arguments

analysis_setup	An object containing directory paths and data tables, produced by the prepare_reads function
cutadapt_path	Path to the 'Cutadapt' program.
overwrite_existing	Logical, indicating whether to remove or overwrite existing files and directories from previous runs. Default is FALSE.

Details

If samples are comprised of two different metabarcodes (like ITS1 and rps10), reads will also be demultiplexed prior to 'DADA2'-specific read trimming steps.

Value

Trimmed reads, primer counts, quality plots, and ASV matrix.

Examples

# Remove remaining primers from raw reads, demultiplex pooled barcoded samples,
# and then trim reads based on specific 'DADA2' parameters
analysis_setup <- prepare_reads(
  data_directory = system.file("extdata", package = "demulticoder"),
  output_directory = tempdir(),
  overwrite_existing = TRUE
)
cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)

demulticoder documentation built on June 8, 2025, 12:47 p.m.