Question: If you only have diploid reference genome, how can you properly assemble a haploid genome?
gravatar for Hranjeev
12 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 11 months ago • written 12 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 12 months ago by Buffo1.2k

edited for clarity.

ADD REPLYlink written 11 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 11 months ago by WouterDeCoster36k
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