Assembly with repetitive regions
I am assembling a synthetic genome sequenced with Oxford Nanopore. The problem is that I obtain a very repetitive assembly with all the contigs such as ATATATATATATATATAT. I do not understand why because I have repeated the process with the Acinetobacter pittii genome, and it seems normal and similar to the reference.
I am new to Oxford Nanopore and assemblies, and although I have read the papers, I cannot understand why this is happening. Is it because the contigs only overlap in repetitive regions, and then the consensus can only use these regions to build the assembly?
Thank you in advance for any help
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