How to check for circularity of contigs that are labeled as linear?

[felince]

Hi,

We recently recieved the complete genome sequence of a bacterium that contains one chromosome and two plasmids assembled with HiFiasm. The chromosome is assembled normaly and it is labeled as circular. On the other hand, the two ～40 kb plasmids are labeled as linear eventhough the ends of each contig,～11kb in one and ～13 kb in the other, have exactly the same sequence. I tried mapping the HiFi reads to the contigs in order to find reads spanning both ends, but each end have different reads mapping to them. One problem is that the coverage for these contigs is around 10x only (for the chromosome is around 40x so this is fine I think), so in my estimation the amount of data obtained is low, compared with what you get using short reads. I don't have much experience with HiFi assemblies, so I wonder if ther was another way to confirm the circularity of such contigs as I think this is probably an assembly error.

Felince