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fastqc website  

FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report to tell if there is anything unusual about your sequence. Each test is flagged as a pass, warning or fail depending on how far it departs from what you'd expect from a normal large dataset with no significant biases. It's important to stress that warnings or even failures do not necessarily mean that there is a problem with your data, only that it is unusual. It is possible that the biological nature of your sample means that you would expect this particular bias in your results.

Required Modules

modules documentation


  • fastqc

System Variables

  • HPC_FASTQC_DIR - installation directory

How To Run

Note that FastQC 0.11 changes how duplication is calculated as described in


  • Validated 4/5/2018