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Old 04-25-2017, 06:41 PM   #20
TomHarrop
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Location: New Zealand

Join Date: Jul 2014
Posts: 20
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Thanks for the suggestions.

It's a TruSeq PCR-free library with an insert size around 470 bp according to the BioAnalyser. I did remove adaptors and contaminants with BBDuk2 (adapters.fa and phix174_ill files that ship with bbtools) but that only removed 0.05% of bases, so maybe I should be look again at the adaptor sequences.

It's a diploid insect. I extracted the DNA from a single, whole individual so there may be some [gut] flora in there... or yes, a repetitive genome, but let's hope not.

PacBio is too expensive for this project and we can't get enough DNA, but I'm looking into getting a MinION for gap closing.
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