Read FASTQ Files — bb_read_fastq • bambamR

Reads FASTQ files using ShortRead (if available) or a minimal base-R parser as fallback. Supports .gz compressed files.

Usage

bb_read_fastq(path, n = NULL)

Arguments

path: Character. Path to a FASTQ or FASTQ.gz file.
n: Integer or NULL. Number of reads to sample. NULL reads all.

Value

A data.frame with columns:

id: Read identifier
sequence: Nucleotide sequence
quality: Quality string (Phred+33 encoded)

Examples

# \donttest{
# Create a temporary FASTQ file
tmp <- tempfile(fileext = ".fastq")
writeLines(c(
  "@read1", "ACGTACGT", "+", "IIIIIIII",
  "@read2", "TGCATGCA", "+", "HHHHHHHH"
), tmp)
reads <- bb_read_fastq(tmp)
reads
#>      id sequence  quality
#> 1 read1 ACGTACGT IIIIIIII
#> 2 read2 TGCATGCA HHHHHHHH
# }