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Old 03-08-2017, 08:43 AM   #20
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Join Date: Apr 2013
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Originally Posted by fanli View Post
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.
I am not interested in a specific genome in the soil community. Basically, I am just interested in the microbial composition and functional content. There is another way that people usually do. They don't assemble or merge pairs and they just blast using raw data. However, I think blast using ~150bp reads is worse. Some publication shows the intermediate length (merged pair) is better than assembled longer reads or unasembled short reads for the question that I am asking for.
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