seeFastq: Quality reports for FASTQ files

In systemPipeR: systemPipeR: NGS workflow and report generation environment

Description

The following seeFastq and seeFastqPlot functions generate and plot a series of useful quality statistics for a set of FASTQ files including per cycle quality box plots, base proportions, base-level quality trends, relative k-mer diversity, length and occurrence distribution of reads, number of reads above quality cutoffs and mean quality distribution. The functions allow processing of reads with variable length, but most plots are only meaningful if the read positions in the FASTQ file are aligned with the sequencing cycles. For instance, constant length clipping of the reads on either end or variable length clipping on the 3' end maintains this relationship, while variable length clipping on the 5' end without reversing the reads erases it.

The function seeFastq computes the summary stats and stores them in a relatively small list object that can be saved to disk with save() and reloaded with load() for later plotting. The argument 'klength' specifies the k-mer length and 'batchsize' the number of reads to random sample from each fastq file.

Usage

seeFastq(fastq, batchsize, klength = 8)

seeFastqPlot(fqlist, arrange = c(1, 2, 3, 4, 5, 8, 6, 7), ...)

Arguments

fastq	Named character vector containing paths to FASTQ file in the data fields and sample labels in the name slots.
batchsize	Number of reads to random sample from each FASTQ file that will be considered in the QC analysis. Smaller numbers reduce the memory footprint and compute time.
klength	Specifies the k-mer length in the plot for the relative k-mer diversity.
fqlist	list object returned by seeFastq().
arrange	Integer vector from 1 to 7 specifying the row order of the QC plot. Dropping numbers eliminates the corresponding plots.
...	Additional plotting arguments to pass on to seeFastqPlot().

Value

The function seeFastq returns the summary stats in a list containing all information required for the quality plots. The function seeFastqPlot plots the information generated by seeFastq using ggplot2.

Author(s)

Thomas Girke

Examples

## Not run: 
targets <- system.file("extdata", "targets.txt", package="systemPipeR")
dir_path <- system.file("extdata/cwl/hisat2/hisat2-se", package="systemPipeR")
args <- loadWorkflow(targets=targets, wf_file="hisat2-mapping-se.cwl", 
                  input_file="hisat2-mapping-se.yml", dir_path=dir_path)
args <- renderWF(args, inputvars=c(FileName="_FASTQ_PATH1_", SampleName="_SampleName_"))
fqlist <- seeFastq(fastq=infile1(args), batchsize=10000, klength=8)
pdf("fastqReport.pdf", height=18, width=4*length(fastq))
seeFastqPlot(fqlist)
dev.off()


## End(Not run)

systemPipeR documentation built on Jan. 26, 2021, 2 a.m.