I am looking for new system for my lab. and I want to know that do typical genomics alignment assembly and annotation tools (specifically tools like BWA, velevet, spades, unicycler, Qiime2) support GPU based parallel processing ?? one of my friend told me to go for good GPU rather than buying new workstation. Any suggestion is highly appreciated.
As far as I know GPUs don't play a big role in bioinformatics. Most software is designed to run on Linux servers, reachable via commandline only - at least in my company the focus is by far more on CPU than GPU. Especially the tools you mention, BWA, SPAdes, Qiime2 are mostly CPU and/or memory intensive. A combination of good CPUs and substantial memory will be more useful than spending money on expensive GPUs.
There are a few GPU projects, eg here https://developer.nvidia.com/Clara-Genomics (interestingly minimap2 is getting the gpu treatment)
and there have been a few in the past, eg. soap3-dp, bwagpu, some accelerated GPU blast-like programs, etc, but in general there hasn't been great uptake in the community.
CPU aligners tend to be fast enough and GPU is still tricky to program for and more tied to rapidly changing hardware. I've had more failures than successes trying to get GPU programs to work.
Oxford nanopore's technology does use a lot of GPUs for basecalling, polishing and now alignment.
GPUs have a place in bioinformatics, but for now it's a small one since there's still so much underexploited CPU power on the table. I'd expect the workstation to be a better investment unless you already know you're bottlenecked on some computation where today's best GPU-exploiting software beats the best non-GPU software by more than an order of magnitude.
I agree on what is said before, GPUs are nice but is not commonly used in Genomics because most software doesn't need it or the cost/benefit is not great. Protein and numerical simulations fit better for GPUs. I have a Tesla in one server, I have never used it for any analysis in the past 3 years.