I just scanned the recent thread started by Abhi Pratap, titled "Experience with Loading NGS data on standalone instance of galaxy"
I didn't see any mention of the SAMtools in that thread. SAMtools is a platform neutral set of formats and programs for next generations sequence data. See http://samtools.sourceforge.net/ for more.
Has the Galaxy team considered adding support for SAMtools formats? It might be a way to deal with all the NGS platforms with a single set of code.
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