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Old 09-10-2016, 09:24 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Are these single-cell libraries or isolate libraries? With isolate libraries there is no reason to expect highly variable coverage and contigs with much lower coverage than normal are most likely contaminants (or "junk"). If they align to the same genus then they are less likely to be contamination and more likely to be ... well, some other variety of thing that you don't want, like assembly from chimeric reads or some other artifact. With single-cell it's much more difficult to determine.
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