run.fastqc.sh

Description

Visualize FastQC output as a PDF, for a batch of samples.

Usage

run.fastqc.sh -s <file> -a <file> -d <directory> -o <directory> -t <positive integer>

Dependencies

fastqc

Arguments

# Required
-s        Path to file with sample names, without header or '>'.
-a        Path to FASTA file with adapter sequences.

# Optional [DEFAULT]
-d        Path to input directory [DEFAULT: $(pwd)]
-o        Path to output directory [DEFAULT: ${in}/fastqc]
-t        Threads [DEFAULT: 16]

Details

FastQC already provides a visualization of the results via .html files. However, if you work with many samples, you'd need to inspect dozens or hundreds of such files manually. CaptureAl provides a concise visualization of up to hundred or more *_fastqc.zip result files, in a single PDF file of 18 pages.

Some plots show the distribution of key statistics across all samples, while other plots show detailled statistics on a per-sample basis using ggplot2 and facets for a direct comparison across samples.

Value

A PDF file with 18 pages. Pages show different read statistics. Different samples are shown on the same page use `ggplot` facetting.

Examples

run.fastqc.sh -s samples.dalbergia.12.txt -d NovaSeq-run1_raw -a adapters.fasta -t 12