fastqc

Summary

• Module Name: fastqc

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Software Description

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.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load fastqc

Depending on where you are working, there may be more than one version of fastqc available. To see which modules are available for loading you can run:

module avail fastqc

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunFASTQCTest_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunFASTQCTest_job.out
#SBATCH --error=rfm_RunFASTQCTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p msismall
module load fastqc/0.11.7
fastqc r1.fq r2.fq