Ok, to be more accurate, I'm trying to determine if an antibiotic resistance gene is whether on the chromosome or in a plasmid of a bacteria. I tried different approaches and I saw that SPAdes was able to generate plasmids,

I tried but was quiet disappointed; I have a strain containing the resistance and a clone strain without it. Using alignment tools (on reads or de novo assembly) no problem to discriminate positive and negative strains, however using plasmidSPAdes I found both strains with my gene... I played with alignment parameters (such as seed,...) but not with SPAdes.

So I would like to have your opinion on that, what can I do? and does anyone of you have used plasmidSPAdes? encountered such problem? or not?

Thanks!