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.

The main functions of FastQC are:

  • Import of data from BAM, SAM or FastQ files (any variant).
  • Providing a quick overview to tell you in which areas there may be problems.
  • Summary graphs and tables to quickly assess your data.
  • Export of results to an HTML based permanent report.
  • Offline operation to allow automated generation of reports without running the interactive application.