GPU sequence aligner

[brianlamx]

Hi all,

Just to let you know that we have released a GPU sequence aligner BarraCUDA based on BWA.

http://seqbarracuda.sf.net

The paper is current in press and will be available very soon early next year. A presentation is available from:

http://www.doc.ic.ac.uk/UKGPU2011/

Cheers

[adaptivegenome]

This looks very exciting. So I saw in your presentation that using a Telsa gives you the performance of 6 Xeon cores?

Does this mean that running your code with a Tesla and 1 CPU core, is equivalent to running it on 7 CPU cores?

Have you tested it on a GTX480?

[brianlamx]

Depends which Xeon processors you are comparing to. A tesla C2070 is about the same as a Xeon X5670 (6 cores) or 25% faster than 2x Xeon X5472 (8 cores).

GTX480 should have more or less the same speed as a tesla C2070.

[yumtaoist]

Great

It's great!

[adaptivegenome]

Depends which Xeon processors you are comparing to. A tesla C2070 is about the same as a Xeon X5670 (6 cores) or 25% faster than 2x Xeon X5472 (8 cores).

GTX480 should have more or less the same speed as a tesla C2070.

Thanks. This sounds really exciting. We will test and let you know how it goes.

[biznatch]

My video card has 2GB VRAM (actually 1899 MB) so I'm guessing there would be no way to to align to the mouse genome (.bwt + .rbwt =~ 1950MB)?

[brianlamx]

Unfortunately no, at least for the current version. You'll need at least a tesla C2050.

[idonaldson]

Is BarraCUDA going to support color-space mapping (SOLiD)?

[brianlamx]

It's BWA based so it should.