I have been dealing for a while about getting draft genome of bacteria. I have chosen a closely related bacteria to make reorder contigs and concatenate them using ABACAS. This closely related bacteria was selected based on phylogenetic tree result. However, the problem is that genome size of organism and size of assembly is different.
After I did this, I visualized circular genome of the species but the size of assembly normally increased and some gaps (NNNNs) occured. Therefore, I am a bit confused If I am on the right way. What do you think about it ? Do you think that this approach is true ? Or, since size of reference genome is bigger than assembly, I could remove gaps in the draft genome in the final step. Does it make sense ?