How to say that something doesn't get divided?

An indivisible cluster is one that cannot or should not be divided. If you feel uneasy about the word there are several other candidates. I only suggest a few here.

Inseparable - one that cannot be separated.

Amalgamated - one in which the individual components have lost their separate identities.

Pooled - one in which the components represent a combined pool with its own identity. This word may be liked for its familiarity, or disliked for its potential to confuse, by genetics specialists because of its echoing of the phrase gene pool.

Bound - one in which the originally separate items are now locked together. (As in the concept of “bound electrons”)

Fixed - one that is fixed together permanently (similar usage to “the fixed stars”)

A late thought: would “immutable” be suitable? An immutable cluster implies one that is permanent and cannot be changed.

“…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.)