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Old 08-29-2017, 12:47 PM   #1
Location: Atlanta

Join Date: Dec 2012
Posts: 70
Default How many reads needed for comparing the genome different bacteria strains.

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.
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Old 08-30-2017, 10:54 AM   #2
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

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.
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