How many reads needed for comparing the genome different bacteria strains.

[illuminaGA]

Dear All

We have a project to identify the different bacteria strains and also want to find the genome different between different strains by WGS method.

The bacteria genome is ~2-3M.

So how many reads or depth I will need?
Do you have any recommended software/pipeline to do this?

Thank you so much.

[Brian Bushnell]

Can you clarify this a lot? It's not clear whether you are looking at a deep ocean metagenome or comparing two isolates of a bacteria with a published reference, each grown in a petri dish. The approaches and tools are completely different so the question cannot be answered without much more detailed information.