I have assembled the plant mitochondrial genome with Canu using Pacbio Sequel data. In the results of assembly, some contigs are entirely tandem repeats. I have no reference sequence and I want to know whether these repeats are real or mis-assembly. Then, all reads were mapped to contig using minimap2 and results were viewed in IGV software. My questions are as follows:

1. In IGV, what kind of evidence can prove that the contig is a mis-assembly?

2. How to prove that a contig is complete and cannot be extended?

Thank you very much