read_prefilt_fastq: A function for calling read_fastq, primer_check, and...

In demulticoder: Simultaneous Analysis of Multiplexed Metabarcodes

A function for calling read_fastq, primer_check, and remove_ns functions. This will process and edit the FASTQ and make them ready for the trimming of primers with 'Cutadapt'. Part of a larger 'prepare_reads' function.

Description

A function for calling read_fastq, primer_check, and remove_ns functions. This will process and edit the FASTQ and make them ready for the trimming of primers with 'Cutadapt'. Part of a larger 'prepare_reads' function.

Usage

read_prefilt_fastq(
  data_directory_path = data_directory_path,
  multithread,
  temp_directory_path
)

Arguments

data_directory_path	The path to the directory containing raw FASTQ (forward and reverse reads), metadata.csv, and primerinfo_params.csv files
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

Returns filtered reads that have no Ns

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