catfastq: Concatenate Fastq Files.

In Rfastp: An Ultra-Fast and All-in-One Fastq Preprocessor (Quality Control, Adapter, low quality and polyX trimming) and UMI Sequence Parsing).

Description

concatenate multiple fastq files into a single file.

Usage

catfastq(output, inputFiles, append = FALSE, paired = FALSE, shuffled = FALSE)

Arguments

output	output file name [string]
inputFiles	a vector of input file names [vector]
append	a logical indicating append the files to a file already exists.
paired	a logical indicating split the input files into two halves. the first half merged into read1, the second half merged into read2.
shuffled	a logical indicating split the input file list into two halves. The R1/R2 files are inteleaved in the inputFiles vector.

Value

no returns.

Author(s)

Wei Wang

Examples

pe001_read1 <- system.file("extdata","splited_001_R1.fastq.gz",
     package="Rfastp")
pe002_read1 <- system.file("extdata","splited_002_R1.fastq.gz",
     package="Rfastp")
pe003_read1 <- system.file("extdata","splited_003_R1.fastq.gz",
     package="Rfastp")
pe004_read1 <- system.file("extdata","splited_004_R1.fastq.gz",
     package="Rfastp")

pe001_read2 <- system.file("extdata","splited_001_R2.fastq.gz",
     package="Rfastp")
pe002_read2 <- system.file("extdata","splited_002_R2.fastq.gz",
     package="Rfastp")
pe003_read2 <- system.file("extdata","splited_003_R2.fastq.gz",
     package="Rfastp")
pe004_read2 <- system.file("extdata","splited_004_R2.fastq.gz",
     package="Rfastp")

allR1 <- c(pe001_read1, pe002_read1, pe003_read1, pe004_read1)
allR2 <- c(pe001_read2, pe002_read2, pe003_read2, pe004_read2)

allreads <- c(allR1, allR2)
allreads_shuffled <- c(pe001_read1, pe001_read2, pe002_read1, pe002_read2,
               pe003_read1, pe003_read2, pe004_read1, pe004_read2)

outputPrefix <- tempfile(tmpdir = tempdir())
# a normal concatenation for single-end libraries.

catfastq(output = paste0(outputPrefix, "_R1.fastq.gz"), inputFiles = allR1)

# a normal concatenation for paired-end libraries.

catfastq(output = paste0(outputPrefix, "merged_paired"),
    inputFiles = allreads, paired=TRUE)

# Append to exist files (paired-end)

catfastq(output=paste0(outputPrefix,"append_paired"), inputFiles=allreads,
    append=TRUE, paired=TRUE)

# Input paired-end files are shuffled.

catfastq(output=paste0(outputPrefix,"_shuffled_paired"),
    inputFiles=allreads_shuffled, paired=TRUE, shuffled=TRUE)

Rfastp documentation built on Nov. 8, 2020, 5:52 p.m.