If you only have diploid reference genome, how can you properly assemble a haploid genome?
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6.9 years ago
Hranjeev ★ 1.5k

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?

Assembly de novo reference-based • 1.6k views
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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.

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edited for clarity.

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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.

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