I'm not a bioinformatitician either, but that repo has some problems, filenames using the : character, a single perl file > 1MB with over 23K lines, a quick glance at which shows room for improvement. I'm not sure if part of the relatively popular Bioperl suite of tools can address your requirements. Regardless all of this is good advice. You don't need to store everything in memory even if you are just planning to call some external command line tool. Consider an alternative such as a database.

In reply to Re^3: System call doesn't work when there is a large amount of data in a hash by marto
in thread System call doesn't work when there is a large amount of data in a hash by Nicolasd

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