Reads in FASTQ file produced by CASAVA 1.8 contain 'N' or 'Y' as a part of an idetifier. 'Y' if a read if filtered, 'N' if the read if the read is not filtered. The workflow cleans up the filtered reads.
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.
The workflow sample "CASAVA FASTQ Filter" can be found in the "Custom Elements" section of the Workflow Designer samples.
The workflow looks as follows:
<center> <br> <img src="/wiki/download/attachments/16122712/CASAVA FASTQ Filter.png"/> <br> </center>