Remove primers using cutadapt — cutadapt_remove

You need to install Cutadapt. See also https://github.com/VascoElbrecht/JAMP/blob/master/JAMP/R/Cutadapt.R for another call to cutadapt from R

Usage

cutadapt_remove_primers(
  path_to_fastq,
  primer_fw = NULL,
  primer_rev = NULL,
  folder_output = "wo_primers",
  nproc = 1,
  pattern = "fastq.gz",
  pattern_R1 = "_R1",
  pattern_R2 = "_R2",
  nb_files = Inf,
  cmd_is_run = TRUE,
  return_file_path = FALSE,
  args_before_cutadapt =
    "source ~/miniconda3/etc/profile.d/conda.sh && conda activate cutadaptenv && ",
  verbose = TRUE
)

Arguments

path_to_fastq: (Required) A path to a folder with fastq files. See list_fastq_files() for help.
primer_fw: (Required, String) The forward primer DNA sequence.
primer_rev: (String) The reverse primer DNA sequence.
folder_output: The path to a folder for output files
nproc: (default 1) Set to number of cpus/processors to use for the clustering
pattern: a pattern to filter files (passed on to list.files function).
pattern_R1: a pattern to filter R1 files (default "R1")
pattern_R2: a pattern to filter R2 files (default "R2")
nb_files: the number of fastq files to list (default FALSE)
cmd_is_run: (logical, default TRUE) Do the cutadapt command is run. If set to FALSE, the only effect of the function is to return a list of command to manually run in a terminal.
return_file_path: (logical, default FALSE) If true, the function return the path of the output folder (param folder_output). Useful in targets workflow
args_before_cutadapt: (String) A one line bash command to run before to run cutadapt. For examples, "source ~/miniconda3/etc/profile.d/conda.sh && conda activate cutadaptenv &&" allow to bypass the conda init which asks to restart the shell
verbose: (logical, default TRUE) If FALSE, suppresses all output from the cutadapt command (stdout and stderr) as well as the completion message. Note: standard R suppression functions (suppressMessages, capture.output) cannot silence system command output; use this parameter instead.

Value

a list of command or if return_file_path is TRUE, the path to the output folder

Details

This function is mainly a wrapper of the work of others. Please cite cutadapt (doi:10.14806/ej.17.1.200 ).

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
cutadapt_remove_primers(system.file("extdata", package = "MiscMetabar"),
  "TTC",
  "GAA",
  folder_output = tempdir()
)

cutadapt_remove_primers(
  system.file("extdata",
    package = "dada2"
  ),
  pattern_R1 = "F.fastq.gz",
  pattern_R2 = "R.fastq.gz",
  primer_fw = "TTC",
  primer_rev = "GAA",
  folder_output = tempdir()
)

cutadapt_remove_primers(
  system.file("extdata",
    package = "dada2"
  ),
  pattern_R1 = "F.fastq.gz",
  primer_fw = "TTC",
  folder_output = tempdir(),
  cmd_is_run = FALSE
)

unlink(tempdir(), recursive = TRUE)
} # }