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Old 12-11-2018, 05:04 AM   #1
smoics
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Default post de novo assembly reference mapping?

I am curious if there is a program/app that would do post de novo assembly reference mapping--essentially breaking down the full scaffold into chunks and reference mapping it post-assembly.

I do recognize that I could alternatively use a software to reference map while doing the initial assembly. Just exploring options.
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Old 12-11-2018, 08:15 PM   #2
SNPsaurus
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The bbtools program shred.sh will break a reference into chunks which can then be used for alignment. I'm not totally sure that is what you are looking for but it is my best bet!
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