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Old 09-23-2014, 11:10 AM   #6
Brian Bushnell
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Location: Walnut Creek, CA

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You still have ~14000x coverage which is way too high. Like I said, you need to target closer to 40x coverage, or at least, no more than 100x.

BLAST your contigs to see what they are, and blast a few unaligned reads to see what those are. You could have massive contamination. And anyway, it seems unlikely that you have 24GB of data on a mitochondria. Why would anyone do that? It's very wasteful experimental design.
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