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Old 12-01-2016, 09:24 AM   #44
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Since you are pulling the kmer information from randomly-sheared metagenomic reads, and using the variable region as a seed, it should be safe. However, there is a possibility of running into a tandem repeat region during extension when you give it a very high extension limit, so I recommend also adding the flag "ibb=f". It probably won't make any difference though.
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