I'm working on a final project for my genomics course. I'd like to analyze the genomes for a few species of Borrelia. However, the assemblies of the genomes seem to be very inconsistent. For example, for Borrelia afzelii, one assembly has 6 chromosomes and plasmids, and another has 10. Another assembly has only one chromosome. Their N50 values are also about the same. So I have no way of knowing which one to choose.
In general, what rules of thumb should I be following when deciding which assembly to use from the NCBI RefSeq database?
Thank You for the help