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Old 03-31-2013, 01:35 PM   #1
NGS_New_User
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Location: USA

Join Date: Sep 2012
Posts: 41
Question Genome comparisons

Hello,

I currently ran a de novo assembly on a male and female genome of a non-model organism.
My plan is to compare the male and female genomes (get percentage of similarity and differences) then extract and annotate the sections that are unique between them.
Additionally, I also plan to align(map) both male and female genomes with a well annotated genome of a related species (model organism); and annotate regions of similarities as well as finding out the percentage of how different or similar they are.

My question is, what are the recommended ngs programs (soft ware) that I should use to accomplish what I want to do?

Any suggestions will be appreciated
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alignment, annotation, de novo assembly, genome comparison

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