Overview
FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
Using
Use the module name fastqc to discover versions available and to load the application.
Multicore
According to the fastqc --help documentation:
-t --threads Specifies the number of files which can be processed
simultaneously. Each thread will be allocated 250MB of
memory so you shouldn't run more threads than your
available memory will cope with, and not more than
6 threads on a 32 bit machine
So, only request as many cores as files you are processing. Example:
#SBATCH --cpus-per-task=2 fastqc -t 2 file1.fastq.gz file2_2.fastq.gz