cut_trim {demulticoder}R Documentation

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
)


[Package demulticoder version 0.1.2 Index]