Subsample a fastq file copying the n_seq first sequences in a given folder

Useful to test a pipeline on small fastq files.

Usage

subsample_fastq(fastq_files, folder_output = "subsample", nb_seq = 1000)

Arguments

fastq_files

The path to one fastq file or a list of fastq files (see examples)

folder_output

The path to a folder for output files

nb_seq

(int; default 1000) : Number of sequences kept (every sequence spread across 4 lines)

Value

Nothing, create subsampled fastq files in a folder

Author

Adrien Taudière

Examples

# \donttest{
ex_file <- system.file("extdata", "ex_R1_001.fastq.gz",
  package = "MiscMetabar",
  mustWork = TRUE
)
subsample_fastq(ex_file, paste0(tempdir(), "/output_fastq"))
subsample_fastq(list_fastq_files(system.file("extdata", package = "MiscMetabar")),
  paste0(tempdir(), "/output_fastq"),
  n = 10
)
unlink(paste0(tempdir(), "/output_fastq"), recursive = TRUE)
# }