I have recently assembled a genome de-novo. I am looking for fertility genes where there is only 1 copy of the gene in the true genome. I am worried that if there are multiple copies of a gene in the true genome, they will appear as a single gene in the de-novo assembly. Is this a reasonable concern? If so, how would I detect this?
Edit - I do not have multiple samples, as many CNV detection tools require. I have only the reads (miSeq, hiSeq, and PacBio) and a reference assembly.