Remove primers from a FASTA database using cutadapt

Removes pairs of primers and flanking regions from a FASTA reference database using cutadapt. Uses linked adapters to trim between forward and reverse primers.

Usage

cutadapt_rm_primers_db(
  ref_fasta,
  output = NULL,
  primer_fw = NULL,
  primer_rev = NULL,
  discard_untrimmed = TRUE,
  nproc = 1,
  verbose = TRUE,
  cmd_is_run = TRUE,
  return_file_path = FALSE,
  start_with_fw = FALSE,
  output_json = FALSE,
  error_tolerance = 0.1,
  args_before_cutadapt = paste0("source ~/miniforge3/etc/profile.d/conda.sh ",
    "&& conda activate cutadaptenv && ")
)

Arguments

ref_fasta

(Character, required) Path to a FASTA file (plain or gzip).

output

(Character) Path to the output FASTA file. If NULL, defaults to {basename}_cutadapted.fasta.

primer_fw

(Character, required) The forward primer DNA sequence.

primer_rev

(Character, required) The reverse primer DNA sequence.

discard_untrimmed

(Logical, default TRUE) Discard sequences where primers were not found.

nproc

(Integer, default 1) Number of CPU cores for cutadapt.

verbose

(Logical, default TRUE) Print summary statistics.

cmd_is_run

(Logical, default TRUE) If FALSE, return the command string without executing it.

return_file_path

(Logical, default FALSE) If TRUE, return the output file path instead of the command.

start_with_fw

(Logical, default FALSE) If TRUE, the forward primer must be anchored at the start of the sequence.

output_json

(Logical, default FALSE) If TRUE, write a JSON summary of the cutadapt process.

error_tolerance

(Numeric, default 0.1) Maximum error rate for primer matching.

args_before_cutadapt

(Character) Shell commands to run before cutadapt (e.g., conda activation).

Value

The cutadapt command string, or the output file path if return_file_path = TRUE.

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_rm_primers_db(
  "database.fasta.gz",
  output = "db_cutadapted.fasta",
  primer_fw = "GCATCGATGAAGAACGCAGC",
  primer_rev = "TCCTCCGCTTATTGATATGC"
)
} # }