Very few of the operations used GPU. Things may have changed since I was working there, but the work at the time wasn't suited for a GPU architecture.
Initial step was sequence cleanup, which is a hidden markov model executed over a collection of sequences of varying length, so hard to parallelize. Sequence annotation is embarassingly parallel on a per-library basis (each sequence can be annotated independently of the other), but the computational work is fuzzy string matching, which is once again hard to GPU-ize. Another major computational job was contig assembly, which is somewhat parallelizable (pairwise sequence comparisons), but once again involves fuzzy string matching so not GPU-izable.
So that's just sequence genetics. Don't know if GPUs are used in other areas.
Lots of cores, lots of threads, and lots of main memory. That was the key.