genome assembly

Question

[a.hafez]

How can I make assembly of the becaterial genome based on reference genome?

what are the recommended tools that can i use them.

[Ram]

assembly ... based on reference genome

Is that a thing? Are you referring to alignment? I think there's also reference guided assembly. Please edit your question as give us as much detail as you can.

[dthorbur]

You could use a tool like chromosemble from the Satsuma2 suite. I suspect there are newer ones available. However, synteny guided reference assembly is speculative at best. You inherit all the errors in the other genome, as well as including regions that are not syntenic among genomes (genomic rearrangements, for example).

But please include more information in your question. Are the bacteria different species, how far to their last common ancestor, strains of the same species, the same strain, etc...?