FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines.
FastQC creates a comprehensive report looking at the composition and quality of a high throughput sequence library. It can operate either as an interactive stand-alone application suitable for use by end users receiving sequence data, or in a non-interactive mode which would be suitable for integrating into a sequencing pipeline.
FastQC is built in Java and should operate on all platforms. You will need to make sure to have a JRE installed and working, preferably the official Sun JRE.