Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation then the choice of reference doesn't have big impact on the result. On the other hand, if the genome size variation is high then the choice of reference is critical to the accuracy of calculated coverage. My question is , how to choose reference in such cases?

  • $\begingroup$ If you have access you should checkout this paper. it answers your question pretty well I think. $\endgroup$ – d_kennetz Nov 21 '19 at 17:24

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