Illumina now have a sequencer for almost every need: S, M, L & XL. There is a helpful table on their website that give instrument specs and an application-by-application estimate of sample numbers that can be
sequenced in run:
Interestingly gene panel's don't appear on HiSeq 2500. We've used this for targeted sequencing to get phenomenal depth on large numbers of samples to look into heterogeneity in cancer. I'd expect anyone wanting to look deeply into populations would benefit in the same way.
There is also a comparison tool on their website to help you find the right sequencer for your lab: helpful table on their website: interested in RNA-seq for DGE and ChIP-seq in cancer genomics? Here are the results:
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