Question: If you only have diploid reference genome, how can you properly assemble a haploid genome?
gravatar for Hranjeev
7 months ago by
Hranjeev1.4k wrote:

Can I not assemble a haploid genome using a diploid as a reference. Should I or should I not?

Is it acceptable to perform mapping based assembly of a haploid using the diploid as reference? Instead, do you start assembling using a de novo strategy?

ADD COMMENTlink modified 6 months ago • written 7 months ago by Hranjeev1.4k

No lo haga compa ๏̯͡๏ . It is a very confusing.. question... I think you have to understand what exactly is the meaning of diploid and haploid genome and what is its function.

ADD REPLYlink written 7 months ago by Buffo1.1k

edited for clarity.

ADD REPLYlink written 6 months ago by Hranjeev1.4k

To start, the reference genome is haploid. You align/map reads to your reference genome. The ploidy doesn't matter while mapping but does matter when you are calling variants, for example.

ADD REPLYlink written 6 months ago by WouterDeCoster31k
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