The Freq Seq Programs

The FASTQ files generated during Illumina sequencing can be analyzed with either a GUI program or a command line application.  Simply follow the links on the right to start using the software.  The source code for these programs is also available.

When running a program, the settings for the analysis are saved in an XML file so that they can be reused in later analyzes or specified without needing to re-enter them every time.  For those unfamiliar with XML, the GUI program can generate and save these files for you.  You simply need to remember that the .xml file which you created contains all the settings (e.g. which barcodes you used, which variants you looked for, etc). 

Advanced users may care to look at the advanced options tab to change the various settings in the XML file.