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Old 03-08-2017, 08:39 AM   #19
Senior Member
Location: California

Join Date: Jul 2014
Posts: 198

Would something like kraken or CLARK not be helpful? Are you trying to assemble and annotate de novo genomes? Or trying to figure out the microbial composition and functional content? I guess my point is you would discard ~40% of your data in the joining process, which may not be necessary depending on your task of interest.
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