Hello, I'm running a sensitivity/specificity study between aligners for my master thesis and I've noticed that BFAST is really slow when reading each one of the 14GB indexes. I have a 24 Core Xeon and the problem is that at some points it only uses 1 CPU instead of the 16 that I specified, why is this? After using blat for so long I'm so happy somebody patched it up. Also what is the deal with reporting negative aligments and not updating the flag field in SAM, can I get a 4 there? It would also be nice if when you set threads to something other than 2n it would tell you its invalid before you have to wait the indexes to load would have saved me a lot of time.
PS:
The only thing missing from BFAST is CUDA support, anybody working on this? How nice would it be if you could do 512 threads at the same time, I'm sure you'll need it with Hi-Seq.. Cloud computing doesn't work if you have to upload 200GB of sequence data every day, a $1000 GPU makes much more sense. You are waisting time trying to run a simple text matching algorithm in a CPU, GPU's sounds better..
PS:
The only thing missing from BFAST is CUDA support, anybody working on this? How nice would it be if you could do 512 threads at the same time, I'm sure you'll need it with Hi-Seq.. Cloud computing doesn't work if you have to upload 200GB of sequence data every day, a $1000 GPU makes much more sense. You are waisting time trying to run a simple text matching algorithm in a CPU, GPU's sounds better..
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