FastQC - A Quality Control application for FastQ files ------------------------------------------------------ Most high throughput sequencers generate output in FastQ format. This format combines the base calls for the sequence which was generated with an encoded quality value for each base which says how confident the sequencer was that the base call generated was correct. Before proceeding with the analysis of a sequence data set it is a good idea to do some basic quality control checks on the raw data to ensure that there are no hidden problems which might be more difficult to detect at a later stage. FastQC is an application which takes a FastQ file and runs a series of tests on it to generate a comprehensive QC report. This will tell you 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. FastQC can be run either as an interactive graphical application which allows you to view results for multiple files in a single application. Alternatively you can run the program in a non interactive way (say as part of a pipeline) which will generate an HTML report for each file you process. FastQC is a cross-platform application, written in java. In theory it should run on any platform which has a suitable java runtime environment. Having said that we've only tested in on Windows, MacOSX and Linux running the Oracle v1.6 to 1.8 JREs. Please let us know what happened if you try running it on other platforms / JREs. Please see the detailed instructions in the INSTALL.txt document to tell you how to get a suitable java version to run FastQC on your system. If you have any comments about FastQC we would like to hear them. You can either enter them into the github bug tracker at: https://github.com/s-andrews/FastQC/issues/ ..or send them directly to simon.andrews@babraham.ac.uk.