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Old 10-02-2017, 07:00 AM   #38
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Location: East Coast USA

Join Date: Feb 2008
Posts: 6,813

You could try changing the ambiguous2= parameter and see how that changes the result. "toss/all" may generate results that look more similar. With very similar genomes you are going to have trouble assigning reads reproducibly. How long are these reads?
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