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).


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