How to say that something doesn't get divided?

Solution 1:

“…or there's another concise way of expressing what I've described?”

As a published molecular biologist and native English speaker I would not use “indivisible”, and certainly not “atomic” to describe your clusters. I find it difficult to see why you need to say anything other than something which I would find unambiguous like:

The genes were sorted in two stages. In the first stage each was assigned to a cluster; in the second stage each cluster was assigned to one of two groups.

If you really think you must, you might modify this to something like:

…permanently assigned to a specific cluster…

…each entire cluster was assigned…

However, rather than clarifying the situation I think you risk sowing doubt in the reader’s mind. Why would the reader imagine that a cluster would be split? (Unless there is something that hasn’t been explained in the question.)