What is FastQC

Modern high throughput sequencers can generate hundreds of millions of sequences in a single run. Before analysing this sequence to draw biological conclusions you should always perform some simple quality control checks to ensure that the raw data looks good and there are no problems or biases in your data which may affect how you can usefully use it.

Most sequencers will generate a QC report as part of their analysis pipeline, but this is usually only focused on identifying problems which were generated by the sequencer itself. FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material.

FastQC can be run in one of two modes. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.