I don't think GBrowse specifically utilizes the GPU. Most of the rendering is performed by Perl scripts which in turn call some C libraries (GD).
I think you'll want to look else where for performance tuning. For example, turning on FastCGI, using mod-perl, and enabling the GBrowse render slaves; look in the GMOD wiki and this list's history for more info regarding those.
I'll comment on my own experiences with working next-gen sequence alignments; others could make their own recommendations.
First, make sure you convert your Sam file to Bam format.
Second, avoid trying to upload the sam or bam file through Custom Tracks. It's fine for smallish files, but bigger files take a long time to process (GBrowse tries to convert Sam to Bam if necessary, then force a sort and index) and may lead to time-outs. I find it's best to put the bam file in a static place and edit the datasource conf to point to it. I've also had reasonable success pointing a URL to a Bam file on a second webserver through the custom track.
Third, use semantic viewing to switch between alignments and coverage plots (> 1kb).
Fourth, if you're really just interested in the coverage, consider converting your alignment coverage to a wig file. The script bamToGBrowse.pl included with Bio::SamTools should be able to do this for you. I also have another program, with a few more options, that you can read about at http://code.google.com/p/biotoolbox/wiki/Pod_bam2wig. There are certainly others out there as well….
From: Halian Vilela <halianlian@...>>
Date: Wed, 9 Mar 2011 09:57:52 -0700
To: "gmod-gbrowse@...>" <gmod-gbrowse@...>>
Subject: [Gmod-gbrowse] Does GPU boost rendering performance ?
I'm having some performance issues with Gbrowse, and I'd like to knwo how could I make it better.
It's installed in a HP Server with 4 Quad-core processors and 10GB ram and I'm still having problems (timeouts, big lags) while rendering some large SAM tracks.
I'm wondering if a powerful GPU would solve this kind of problem or the bulk load of the software is really over the CPU+RAM ? Should I get a GPU to try to smooth the rendering process ?
Please any information will be greatly appreciated.