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.
How to Use This Sample
If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation.