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.

To run this software interactively in a Linux environment run the commands:

module load fastqc

FastQC can also be run from the command line.  For a list of options, type the command:

fastqc -help
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