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Old 12-14-2011, 07:18 AM   #4
adaptivegenome
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Join Date: Nov 2009
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If you are going to examine every read in order then I suppose you could parse a giant text file. This sort of sequential analysis is hard to speed up unless you parallelize it. If you are parsing a text file you could break it into many parts and then run your PERL script on the many parts in parallel (if you have access to that kind of equipment).

I am not aware of an off the shelf tool. Sorry!

Personally I opt for pthreads and C/C++...
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