FastQC

Introduction

FastQC is a quality control tool for massive parallel high throughtput sequencing data. It provides a series of metrics that could be used to evaluate the overall quality of data and identify possible problems that should be corrected before any downstream analysis.

Requirements

FastQC is available as a module on Delta and Illinois Campus Cluster (ICC). Requirements are loaded automatically when the module is called:

module load fastqc

Usage

The following SLURM batch script can be used as a template for processing multiple samples with FastQC:

# Path to Working Directory

myWorkDir="/path/to/my/working/directory"
cd $myWorkDir

## -- Reserve a folder for placing the FASTq files. For example: $myWorkDir/seqs/*.fastq (required)
## -- Reserve a folder for storing the reports provided by FASTQC. For example: $myWorkDir/fqc_reports

# Run FASTQC

mkdir -p $myWorkDir/fqc_reports
fastqc -o $myWorkDir/fqc_reports/ $myWorkDir/seqs/*.fastq

References

Andrews S. (2010). FastQC: a quality control tool for high throughput sequence data. Available online at: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/