Building a reference genome for pop differentiation.

Question

[Adrian Pelin]

Hello,

If I have sequenced several isolates of one species but no good reference is available, is it a good idea to try and generate a master assembly using all isolates, and then by mapping to quantify population differentiation between the different isolates?

Or is it a better idea to assemble them separately, take the best assembly and then map other strains to it?

Thank you,

Adrian

Answer 1

[Zev.Kronenberg]

I would suggest latter approach. With the first approach you might get undesirable chimeric contigs. If it isn't computationally limiting you might just want to try both approaches and see which one generates results that are sensible.