collapse.fastq: Very fast fastq/fasta collapser

In JokingHero/ORFik: Open Reading Frames in Genomics

Very fast fastq/fasta collapser

Description

For each unique read in the file, collapse into 1 and state in the fasta header how many reads existed of that type. This is done after trimming usually, works best for reads < 50 read length. Not so effective for 150 bp length mRNA-seq etc.

Usage

collapse.fastq(
  files,
  outdir = file.path(dirname(files[1]), "collapsed"),
  header.out.format = "ribotoolkit",
  compress = FALSE,
  prefix = "collapsed_"
)

Arguments

files	paths to fasta / fastq files to collapse. I tries to detect format per file, if file does not have .fastq, .fastq.gz, .fq or fq.gz extensions, it will be treated as a .fasta file format.
outdir	outdir to save files, default: file.path(dirname(files[1]), "collapsed"). Inside same folder as input files, then create subfolder "collapsed", and add a prefix of "collapsed_" to the output names in that folder.
header.out.format	character, default "ribotoolkit", else must be "fastx". How the read header of the output fasta should be formated: ribotoolkit: ">seq1_x55", sequence 1 has 55 duplicated reads collapsed. fastx: ">1-55", sequence 1 has 55 duplicated reads collapsed
compress	logical, default FALSE
prefix	character, default "collapsed_" Prefix to name of output file.

Value

invisible(NULL), files saved to disc in fasta format.

Examples

fastq.folder <- tempdir() # <- Your fastq files
infiles <- dir(fastq.folder, "*.fastq", full.names = TRUE)
# collapse.fastq(infiles)

JokingHero/ORFik documentation built on Dec. 21, 2024, 12:01 a.m.