Fastp: adapter detection, quality control and preprocessing of FASTQ files

This function is a wrapper for the fastp software to perform quality control and preprocessing of FASTQ files (paired-end or single-end).

To install fastp on Linux:

wget http://opengene.org/fastp/fastp
chmod a+x ./fastp
sudo mv fastp /usr/local/bin/

For other OS or specific installation instructions, please refer to the official fastp GitHub repository: https://github.com/OpenGene/fastp.

Usage

fastp(
  path_to_fastq,
  folder_output = "fastp_output",
  nproc = 1,
  pattern = "fastq.gz",
  pattern_R1 = "_R1",
  pattern_R2 = "_R2",
  nb_files = Inf,
  paired_end = TRUE,
  cmd_is_run = TRUE,
  return_file_path = FALSE,
  qualified_quality_phred = 20,
  average_qual = 20,
  length_required = 50,
  detect_adapter = TRUE,
  trim_poly_g = TRUE,
  correction = TRUE,
  cut_front = TRUE,
  cut_tail = TRUE,
  cut_window_size = 4,
  cut_mean_quality = 20,
  extra_fastp_args = ""
)

Arguments

path_to_fastq: (required) Path to the directory containing FASTQ files. See list_fastq_files() for help.
folder_output: Name of the output folder (default: "fastp_output").
nproc: Number of threads to use (default: 1).
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)
paired_end: Logical, whether files are paired-end (default: TRUE).
cmd_is_run: Logical, whether to run the command (default: TRUE). If FALSE, the only effect of the function is to return a list of commands to run manually in a terminal.
return_file_path: Logical, whether to return output file paths (default: FALSE). Useful in targets workflows.
qualified_quality_phred: Minimum base quality (default: 20).
average_qual: Minimum average read quality (default: 20).
length_required: Minimum read length after trimming (default: 50).
detect_adapter: Logical, enable automatic adapter detection for paired-end reads (default: TRUE).
trim_poly_g: Logical, trim poly-G tails (default: TRUE).
correction: Logical, correct mismatches in overlapped paired-end reads (default: TRUE).
cut_front: Logical, trim low quality bases from 5' end (default: TRUE).
cut_tail: Logical, trim low quality bases from 3' end (default: TRUE).
cut_window_size: Window size for sliding quality filter (default: 4).
cut_mean_quality: Minimum mean quality for trimming window (default: 20).
extra_fastp_args: Additional fastp arguments as a character string (default: "").

Value

If cmd_is_run = FALSE, a named list of fastp commands. If return_file_path = TRUE, a list of output file paths. Otherwise NULL invisibly, after running fastp.

Details

This function is a wrapper for the fastp software, please cite fastp (doi:10.1093/bioinformatics/bty560 ) if you use this function.

Author

Adrien Taudière

Examples

if (FALSE) { # \dontrun{
# Paired-end example
fastp(
  path_to_fastq = system.file("extdata", package = "MiscMetabar"),
  folder_output = file.path(tempdir(), "qc_data"),
  nproc = 8,
  paired_end = TRUE
)

# Single-end example with extra options
fastp(
  path_to_fastq = "raw_data/",
  folder_output = file.path(tempdir(), "qc_data"),
  nproc = 8,
  paired_end = FALSE,
  extra_fastp_args = "--merge --n_base_limit 5 --dedup"
)

# Only build the commands, do not run them
fastp(
  path_to_fastq = system.file("extdata", package = "MiscMetabar"),
  cmd_is_run = FALSE
)
} # }