Hi John,

I have to admit I might not fully understand what you want. I guess you want to see which isolate derived from the other?

If so I would give MUMmer a try to align the individual assemblies.

What you could also do, if your isolates are not too far apart is to map each isolate to each of the assemblies and call SNPs. In this way you can check and avoid mapping biases. I just did this in a study using my mapper: NextGenMap.

Let me know how it goes and if I understood what you want.

Cheers

Fritz

Dear Fritz,

Thanks for your response. I'll give it a try in the mean time and also try your NextGenMap if I can get a good result. 

What I actually want to do is to determine if the Serratia marcescens isolates belong/ originate from the same clone/type. Normally, PFGE would have been used for such a typing exercise. There're no MLST schemes for Serratia. So I would want to know if the type/clonality/relatedness of the isolates can be determined with my WGS data without reverting to PFGE or Rep-PCR. Please have I clarifoed enough ?

Thanks for your help.

John

Dear John,

yes I think I understood what you want. I think I would do the mapping of the reads to the assemblies and then look at the somatic/ shared mutations. These ratios should give you an idea if they originated from the same clone. 

If nearly all SNPs are shared -> they belong to the same clone. The tricky question remains where to draw the cutoff, but I guess you will have an estimate how diverse the organism is. 

Cheers

Fritz