remove_ns: Wrapper function for core 'DADA2' filter and trim function...

In demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

Wrapper function for core 'DADA2' filter and trim function for first filtering step

Description

Wrapper function for core 'DADA2' filter and trim function for first filtering step

Usage

remove_ns(fastq_data, multithread, temp_directory_path)

Arguments

fastq_data	A data.frame containing the read file paths and the direction of the reads by sample
multithread	(Optional). Default is FALSE. If TRUE, input files are filtered in parallel via mclapply. If an integer is provided, it is passed to the mc.cores argument of mclapply. Note that the parallelization here is by forking, and each process is loading another fastq file into memory. This option is ignored in Windows, as Windows does not support forking, with mc.cores set to 1. If memory is an issue, execute in a clean environment and reduce the chunk size n and/or the number of threads.
temp_directory_path	User-defined temporary directory to output unfiltered, trimmed, and filtered read directories throughout the workflow

Value

Return prefiltered reads with no Ns

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