Question: Any returns on plasmidSPAdes?
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gravatar for vmicrobio
11 months ago by
vmicrobio230
France
vmicrobio230 wrote:

Hi!

I'm trying to distinguish plasmid from chromosomic sequences in bacteria. Does anyone have experience using plasmidSPAdes?

Thanks!

plasmid assembly de novo • 335 views
ADD COMMENTlink modified 10 months ago • written 11 months ago by vmicrobio230

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ADD REPLYlink written 11 months ago by h.mon21k
0
gravatar for vmicrobio
10 months ago by
vmicrobio230
France
vmicrobio230 wrote:

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!

ADD COMMENTlink written 10 months ago by vmicrobio230
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