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Old 09-10-2016, 10:36 PM   #4
Brian Bushnell
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Location: Walnut Creek, CA

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"coverage much lower than normal" is on a per-library basis; you can't have a single cutoff value that's always appropriate. That said, while it's difficult to make strict rules... if a contig has coverage under 25% of the median coverage, in an isolate, it's probably best to discard it. Bear in mind, though, that bacterial isolates can have differential coverage by up to ~50% biased toward the origin of replication if you gathered the DNA during exponential growth phase.
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