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FastQC

FastQC is a tool for performing quick quality control checks on raw high-throughput sequencing data, helping identify potential issues before downstream analysis. It supports common sequencing formats and generates clear summary metrics and HTML reports, including in fully offline and automated workflows.

Availability

Cluster Module/Version
BOSE fastqc/0.12.1
BGSC N/A

Note: You can simply use module load fastqc to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the fastqc command that we wanted to highlight. Use the official documentation or this online man page for a full list.

Option Description
--help Display the help file
--outdir Output files to an existing directory
--format Manually set the sequence file format. Formats include bam, sam, bam_mapped, sam_mapped, and fastq
--threads Specify the number of files to concurrently process
--kmers Set the length of Kmer to find. Value between 2 and 10; defaults to 5
--quiet Suppress output, reporting only errors

How To Access

Access to FastQC is available through both Desktop Mode in Open OnDemand and through command line.

Desktop Mode

  1. Log into Open OnDemand - https://ondemand.hpc.uwec.edu
  2. Click "Desktop" on the dashboard, or by first clicking "Interactive Apps" in the top bar.
  3. Fill out your required resources to the best of your abilities. Unsure what to use?
  4. Wait for the job to start, then click "Launch Desktop"
  5. Start the terminal by clicking on the black square icon in the top bar, or by going to Applications --> System Tools --> MATE Terminal"
  6. Type: module load fastqc
  7. Type: fastqc

Command Line

  1. Log into BOSE.
  2. Launch an interactive session or use a Slurm script.
  3. module load fastqc
  4. fastqc inputfile.fastq

Sample Slurm Script

submit.sh
#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load fastqc/0.12.1    # Load FastQC
fastqc inputfile.fastq

Real Example

Has your research group used FastQC in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please cite this project in your papers to support continued development of FastQC. In this GitHub issue, the author recommends citing the project page:

https://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Resources