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 |
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 |
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]