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FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.

Fastqc is available as a module on Apocrita.


To run the default installed version of Fastqc, simply load the fastqc module:

$ module load fastqc
$ fastqc --help
            FastQC - A high throughput sequence QC analysis tool


        fastqc seqfile1 seqfile2 .. seqfileN

    fastqc [-o output dir] [--(no)extract] [-f fastq|bam|sam]
           [-c contaminant file] seqfile1 .. seqfileN

Example job

Serial job

Here is an example job running on 1 core and 1GB of memory:

#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load fastqc

fastqc raw_data.fastq.gz raw_data2.fastq.gz

Viewing the Fastqc results

To view the Fastqc results, you may open the fastqc_report.html file in a web browser or the summary.txt file (located in the zipped output archive) on the command line. For assistance copying files to your local machine, please see the Moving Data page.