If you only have diploid reference genome, how can you properly assemble a haploid genome?
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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.
edited for clarity.
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.