actual use of GPGPUs

[mkeehan]

Is anyone actually successfully using GPGPU based hardware for next Gen Sequencing use?

I've heard of one organisation using GPU-HMMER but is there anyone using a GPGPU package for short read mapping?

A brief mention of hardware/software and approximate speedup would be nice.

Thanks

Mike

[john_mu]

This greatly depends on the type of data you wish to map. In my opinion, with the current types of short reads there is not much speed up to be gained from using GPGPU. Hence, as far as I know nobody has been bothered to make an implementation.

One related example is

http://www.nvidia.com/object/mummer_on_tesla.html

however it is kind of specialized since it for bacterial genomes.