Question: If you only have diploid reference genome, how can you properly assemble a haploid genome?
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gravatar for Hranjeev
2.1 years ago by
Hranjeev1.5k
Malaysia
Hranjeev1.5k 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 24 months ago • written 2.1 years ago by Hranjeev1.5k

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 2.1 years ago by Buffo1.8k

edited for clarity.

ADD REPLYlink written 24 months ago by Hranjeev1.5k

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 24 months ago by WouterDeCoster42k
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