The sole reason for requiring fastq-sanger input to all of our wrappers was to force the users to run their data through the groomer. It is slow, but it checks data consistency in a way that is more robust than just checking 'four lines per fastq block' and prevents a lot of problems downstream. Here on Galaxy @ Penn State we see a lot of fastq files edited in MS Word and other similar horrors, which are being caught by groomer and prevent users from running into problems later on (and so cutting down on the support overhead - investigating why groomer has failed is a lot easier than researching why a particular set of polymorphisms derived from a Word-edited fastq file clusters Ukrainians with parasitic worms). In addition, even though Illumina did switch to Sanger encoding, there is still a lot of old data out there. However, we are open to suggestions ... What we are thinking of lately is switching to unaligned BAM for everyting. One of the benefits here is the ability to add readgroups from day 1 simplifying multisample analyses down the road.

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