Hello, With the recent upgrade to CASAVA 1.8, Illumina's FASTQ files now contain both filtered and non-filtered reads (i.e. high and low quality reads, what used to be called "reads that passed filtering"). Here's a program (+galaxy wrapper) that can filter those FASTQ files, preparing them for the down-stream genome mapping programs (Probably a temporary fix until mapping programs add a feature to ignore those reads). http://cancan.cshl.edu/labmembers/gordon/fastq_illumina_filter/ Comments are welcomed, -gordon