Main command to trim primers using Cutadapt and core DADA2 functions

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.

Value

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

Details

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

Examples

if (FALSE) { # \dontrun{
# 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(),
  tempdir_path = tempdir(),
  tempdir_id = "demulticoder_run_temp",
  overwrite_existing = TRUE
)
cut_trim(
analysis_setup,
cutadapt_path="/usr/bin/cutadapt",
overwrite_existing = TRUE
)
} # }