By Matthew Dublin
CLC Bio and Sciengines have announced a collaboration to offer users Sciengines' RIVYERA FPGA-based platform with BLASTp, BLASTn, and Smith-Waterman.
The RIVYERA hardware platform allows the BLAST implementation — which is still under development — on 128 FPGAs that can be set up in each compute unit. An early version of this solution will be showcased at the International Plant & Animal Genome (PAG XX) conference on January 14-18 in San Diego.
According to Jost Bissel, chief software architect at Sciengines, the initial results from running CLC's tuned BLASTp on their FPGA solution demonstrated a 188 times speed up using 64 FPGAs when compared to a Xeon core processor. "The benchmark ran BLASTp to align 920000 amino acids against a database of 1 billion amino acids. Similar acceleration has been achieved in early benchmark tests of the BLASTn version, and we expect both BLAST implementations to be accelerated even further before the final release," says Bissel.
Also at the PAG XX conference, Pico Computing will demonstrate their FPGA-accelerated BFAST solution which is running on its M-502 FPGA modules. According to their white paper, this BFAST implementation is 100 times faster than BFAST running in software and ten times faster than Bowtie. The FPGA system maps 92 percent of short reads versus 85 percent of reads mapped for Bowtie. This sensitivity can be further tuned in the FPGA system. In addition, Pico integrated their FPGA system with Geneious Pro's plugin API to create a visualization and analysis interface.
Timelogic, Mitrionics, Convey, and SGI, have also released FPGA BLAST implementations, but it's difficult to really compare FPGA BLAST solutions against each other — every offering out has a unique hardware configuration — but all FPGAs provide impressive results when compared to a CPU.